title: B90 Epo-Ctrl

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39967.gif
Disease State: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1320, 8800; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 87467; Parameter Laser Power = 1.36; Parameter Scan Time = 10:19:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.85; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 730; Parameter Scan Power = 100; Parameter Laser on time = 452576; Parameter Laser Power = 2.36; Parameter Scan Time = 10:19:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.85; Performer: Minnie,,Sarwal

source_name: B90 Epo-Ctrl

tag: B90 Epo-Ctrl


title: uninfected npr1 Susceptibility T0 npr1 duplicate

status: Public on Oct 21 2008

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18326.gif
Disease State: uninfected
Genotype: npr1

hyb_protocol: not provided

scan_protocol: not provided

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: Arabidopsis thaliana

source_name: Common Reference

label_protocol: not provided

extract_protocol: not provided

tag: Common Reference


title: EpoB67HBP

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38778.gif
Disease State: B67

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 720, 9000; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-02-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 74371; Parameter Laser Power = 1.37; Parameter Scan Time = 11:04:33; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.91; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-02-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 439486; Parameter Laser Power = 2.06; Parameter Scan Time = 11:04:33; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.91; Performer: Minnie,,Sarwal

organism: Homo sapiens

source_name: aRNA pool 20cell lines from PB lab labeled 030503


title: T47D_MTVL_controlsh_+Dox_repl_C

status: Public on Oct 20 2008

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

source_name: T47D-MTVL human breast cancer cell line, control sh, Dox treated

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

growth_protocol: These cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.

tag: H1.2 (and control) knock-down cell lines were established from T47D-MTVL cells

value: Human breast cancer cell line T47D modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named T47D-MTVL (Truss, M., J. Bartsch, A. Schelbert, R. J. Hache, and M. Beato. 1995).

tag: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva) (Wiznerowicz M & Trono D (2003) Conditional suppression of cellular genes

value: lentivirus vector-mediated drug-inducible RNA interference. J Virol 77:8957-8961).

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: T47D_MTVL_controlsh_+Dox_repl_A


title: HCC1143_PAVIN_D07

status: Public on Nov 14 2008

type: genomic

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

description: PAVIN_p_STY33_Mapping250K_Sty_D07_128902

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Copy numbers were estimated by the pre-processing module

label: biotin

molecule: genomic DNA

source_name: human breast

label_protocol: Affymetrix standard procedure

growth_protocol: Cell lines were propagated in growth media recommended by the American Type Tissue Collection

extract_protocol: Genomic DNA was extracted with the DNeasy blood and tissue kit (Qiagen) according to manufacturer's instructions

tag: breast ductal adenocarcinoma


title: T47D_MTVL_controlsh_-Dox_Repl_A

source_name: T47D-MTVL human breast cancer cell line, control sh, Dox untreated


title: T47D_MTVL_controlsh_Repl_D


title: T47D_MTVL_controlsh_-Dox_Repl_B


title: uninfected wt Susceptibility T0 Col0

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17459.gif
Disease State: uninfected
Genotype: wt

source_name: Col-0 common reference

tag: Col-0 common reference


title: B65 Epo-HBP5

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41766.gif
Disease State: B65

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1360, 9120; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 100215; Parameter Laser Power = 1.47; Parameter Scan Time = 10:10:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.43; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 465323; Parameter Laser Power = 1.98; Parameter Scan Time = 10:10:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.43; Performer: Minnie,,Sarwal

source_name: aRNA by SH on 3/27/03 from cell lines

tag: aRNA by SH on 3/27/03 from cell lines

source_name: B65 Epo-HBP5

tag: B65 Epo-HBP5


title: B18 Epo-Ctrl

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39970.gif
Disease State: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1240, 9120; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 660; Parameter Laser on time = 87497; Parameter Laser Power = 1.30; Parameter Scan Time = 10:50:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.13; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 452606; Parameter Laser Power = 2.43; Parameter Scan Time = 10:50:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.13; Performer: Minnie,,Sarwal

source_name: B10 Epo-Ctrl misnamed at submission

tag: B10 Epo-Ctrl misnamed at submission


title: B92 Epo-HBP

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39966.gif
Disease State: B92

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1240, 8960; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 87452; Parameter Laser Power = 1.46; Parameter Scan Time = 10:04:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.71; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 750; Parameter Scan Power = 100; Parameter Laser on time = 452561; Parameter Laser Power = 2.36; Parameter Scan Time = 10:04:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.71; Performer: Minnie,,Sarwal

source_name: B92 Epo-HBP

tag: B92 Epo-HBP


title: Uvula normal squamous epithelium of the uvula VUMC_uvula6_b7_s

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: normal squamous epithelium of the uvula of a non-cancer patient who underwent uvulopalatopharyngoplasty

hyb_protocol: Slides were pre-hybridised for 45 minutes at 37°C with a pre-hybridisation solution containing 30 micrograms of salmon sperm DNA (Gibco), 12 micrograms of poly A (Pharmacia), 60 micrograms of yeast tRNA (Sigma) and 24 micrograms of Cot-1 DNA (Invitrogen) dissolved in 127 microliter hybridisation mix (0.2% SDS, 8% glycerol, 50% formamide and 0.1% dextrane sulphate in 2x SSC). Pre-hybridisation was followed by probe hybridisation for 14 hours at 37°C. Both pre-hybridisation and hybridisation were performed in HybStation 12 (Perkin Elmer Life Sciences)

scan_protocol: as described by Buermans et al, Physiol Genomics, volume 21 (3), p 314-23

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. Microarray data were normalised using Lowess regression. When both intensities were below 50, hybridisation was assumed inefficient and the ratio value was considered ‘missing’. The cut-off “50” is based on technical reproducibility: intensities above 50 were reasonably reproducible for technical replicates on our platform. To obtain more stable ratios, intensity values below 50 were substituted by 50 when the other channel was above 50. Genes with missing ratio values in more than 20% of arrays were excluded from analysis. Remaining missings were imputed using K-nearest neighbour imputation.

source_name: uvula

label_protocol: cDNA was prepared from 15 micrograms of total RNA using oligo-dT20-VN primer (Invitrogen) and coupled to Cy3 by enzymatic labelling with dUTP-Cy3

extract_protocol: TRIzol according to manufacturers' instructions

tag: normal squamous epithelium of the uvula

source_name: universal human reference RNA (Stratagene)

label_protocol: as ch1, Cy5 in stead of Cy3

extract_protocol: see www.stratagene.com

tag: Pooled RNA of 10 cell lines giving broad gene coverage


title: B55 Epo-HBP3

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41762.gif
Disease State: B55

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1320, 9560; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 101493; Parameter Laser Power = 1.46; Parameter Scan Time = 09:45:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.02; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 466602; Parameter Laser Power = 1.97; Parameter Scan Time = 09:45:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.02; Performer: Minnie,,Sarwal

source_name: B55 Epo-HBP3

tag: B55 Epo-HBP3


title: gura_sed_fum_BR3B

city: Amherst

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geotalea uraniireducens Rf4

source_name: Sediment, BR3B

label_protocol: total RNA was amplified using the Ambion MessageAmp II- Bacteria kit for polyadenylation and subsequent amplification of total RNA. aRNA was ethanol precipitated and resuspended in nuclease-free water to a total concentration of ~1 ug/ul.  Used Micromax ASAP direct RNA labeling protocol.

growth_protocol: Geobacter uraniumreducens Rf4 was grown to mid-log anaerobically in acetate amended Rifle sediment batch cultures.

extract_protocol: For reference see:In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol. 2004 Dec;70(12):7251-9. PMID: 15574924

source_name: Fumarate, BR3B

growth_protocol: Geobacter uraniumreducens Rf4 was grown to mid-log anaerobically in batch cultures with acetate as the electron donor and fumarate as the electron acceptor.


title: B20 Epo-Ctrl2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39969.gif
Disease State: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1080, 9200; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 86348; Parameter Laser Power = 1.46; Parameter Scan Time = 11:19:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.58; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 451457; Parameter Laser Power = 2.28; Parameter Scan Time = 11:19:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.58; Performer: Minnie,,Sarwal

source_name: B20 Epo-Ctrl2

tag: B20 Epo-Ctrl2


title: B20 Epo-Ctrl

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39968.gif
Disease State: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1240, 9280; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 87484; Parameter Laser Power = 1.33; Parameter Scan Time = 10:36:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.05; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 452592; Parameter Laser Power = 2.38; Parameter Scan Time = 10:36:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.05; Performer: Minnie,,Sarwal

source_name: B20 Epo-Ctrl

tag: B20 Epo-Ctrl


title: gura_sed_fum_BR3A

source_name: Sediment, BR3A

tag: grown to mid-log anaerobically in acetate amended Rifle sediment batch cultures

source_name: Fumarate, BR3A

tag: grown to mid-log anaerobically in batch cultures with acetate as the electron donor and fumarate as the electron acceptor


title: Uvula normal squamous epithelium of the uvula VUMC_uvula1_b7_s


title: T47D_MTVL_controlsh_-Dox_Repl_C

source_name: Universal human reference RNA Stratagene® (cat.no.740000)


title: B55 Epo-HBP4

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41763.gif
Disease State: B55

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1560, 9280; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 99832; Parameter Laser Power = 1.37; Parameter Scan Time = 09:58:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.76; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 464940; Parameter Laser Power = 2.03; Parameter Scan Time = 09:58:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.76; Performer: Minnie,,Sarwal

source_name: B55 Epo-HBP4

tag: B55 Epo-HBP4


title: B65 Epo-HBP4

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41765.gif
Disease State: B65

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1280, 9600; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 100199; Parameter Laser Power = 1.44; Parameter Scan Time = 09:55:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.24; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 465308; Parameter Laser Power = 1.94; Parameter Scan Time = 09:55:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.24; Performer: Minnie,,Sarwal

source_name: B65 Epo-HBP4

tag: B65 Epo-HBP4


title: gura_sed_fum_BR1A

source_name: Sediment, BR1A

source_name: Fumarate, BR1A


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC39_b7_s12

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 40 years, contains Human Papilloma Virus type 33

source_name: uterine cervix

tag: squamous cell carcinoma


title: gura_sed_fum_BR1B

source_name: Sediment, BR1B

source_name: Fumarate, BR1B


title: Uvula normal squamous epithelium of the uvula VUMC_uvula8_b7_s

source_name: uvula


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC27_b7_s18

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 49 years, contains Human Papilloma Virus type 69

source_name: universal human reference RNA (Stratagene)


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC4_b7_s4

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 62 years, contains Human Papilloma Virus type 67


title: gura_sed_fum_BR2B

source_name: Sediment, BR2B

source_name: Fumarate, BR2B


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC28_b7_s8

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 48 years, contains Human Papilloma Virus type 35


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC38_b7_s19

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 51 years, contains Human Papilloma Virus type 16


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC32_b7_s9

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 37 years, contains Human Papilloma Virus type 16


title: T47D_MTVL_controlsh_+Dox_repl_B

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

source_name: T47D-MTVL human breast cancer cell line, control sh, Dox treated

tag: H1.2 (and control) knock-down cell lines were established from T47D-MTVL cells

tag: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva) (Wiznerowicz M & Trono D (2003) Conditional suppression of cellular genes

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC2_b7_s3

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 39 years, contains Human Papilloma Virus type 16


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC38_CGHb14_s29

hyb_protocol: Hybridisations were performed as described by Snijders et al, Nat Genetics, volume 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 – Perkin Elmer Life Sciences).

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.

extract_protocol: as described in Wilting et al, J Pathol, volume 209, p 220-30

source_name: Reference DNA

tag: Pooled DNA from the blood of 10 normal male individuals


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC4_CGHb12_s48

label_protocol: as described by Snijders et al, Nat Genetics, volume 29, p 263-4


title: H1.5 sh +dox repl.2

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: Histone H1.5 depletion by RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.5 shRNA expression vector (pLVTHM) induced by doxycyclin

hyb_protocol: For each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after the bead arrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in a Illumina Beadstation.

scan_protocol: The Beadscan software was used to control de scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using BeadStudio software Gene Expression module and the summary data file was processed using the PILLA web einterface tool (Lozano et al, unpublished), an implementation of the Lumi package (Du et al, 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 100 permutations to detect statistically significant differences in gene expression between treated and control conditions (Tusher et al, 2001).

label: biotin / streptavidin-Cy3

source_name: Histone H1.5 shRNA vector; induced by doxycyclin treatment

label_protocol: For each sample 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 9.2 and 9.8.

treatment_protocol: Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva). The 64-mer oligonucleotides for histone H1 shRNA cloning into MluI/ClaI-digested pLVTHM were designed, annealed and phosphorylated as communicated by D. Trono (http://tronolab.epfl.ch/). Oligonucleotides have the following general structure: 5'-CGCGTCCCC-N19 TTCAAGAGA-rcN19-TTTTTGGAAAT-3' and 5'-AGGGG-N19-AAGTTCTCT-rcN19-AAAAACCTTTAGC-3', being N19 the specific target sequence for each H1 variant and rcN19 its reverse complementary sequence. The corresponding 19-mer gene-specific target sequences for interference were designed manually following standard rules (AAN19, GC % 30-70). Target sequences (N19) are CGCTGACTCGCAGATCAAG for H1.0, AGAGCGTAGCGGAGTTTCT for H1.2, CTGCCAAGAGTCCAGCTAA for H1.3, GAAGAGCGCCAAGAAGACC for H1.4 and GGCAACTAAGAAGGCTGCC for H1.5.  For the production of viral particles containing the HIV-derived vectors, 2.5x106 HEK 293T cells (Clontech) were transfected with plasmids ptTR-KRAB-Red, pLVTHM-shH1.n or pEV833-HA-H1.n (10µg), pCMV-R8.91 (6.5µg) and pMD.G (3.5µg) in 10 cm dishes using calcium phosphate. Medium was collected every 24 hours for 2 days and centrifuged 1h30min at 26.000 rpm at 4ºC in a sucrose gradient to concentrate viruses. Pellet containing viral particles was dissolved in medium and used for cell infection. Cells were infected using the spinoculation method, i.e. plates were centrifuged at 1,200 x g for 2 hr at 25 ºC.  Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated. Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.

tag: T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

tag: Histone H1.5 depletion

tag: Histone H1.5 shRNA vector

tag: induced by doxycyclin treatment


title: H1.5 sh -dox repl.1

description: Negative control for histone H1.5 RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.5 shRNA expression vector (pLVTHM) uninduced

source_name: Histone H1.5 shRNA vector; uninduced, no doxycyclin treatment

tag: no depletion

tag: uninduced, no doxycyclin treatment


title: H1.5 sh -dox repl.2

description: Negative control for histone H1.5 RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.5 shRNA expression vector (pLVTHM) uninduced


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC36_CGHb12_s67

description: moderately differentiated squamous cell carcinoma of the cervix, patient age 72 years, contains Human Papilloma Virus type 16


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC39_CGHb12_s68


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC15_b7_s7

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 47 years, contains Human Papilloma Virus type 16

tag: Pooled RNA of 10 cell lines giving broad gene coverage


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC13_b7_s6

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 44 years, contains Human Papilloma Virus type 16


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC28_CGHb12_s65


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC36_b7_s11


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC32_CGHb12_s66


title: H1.5 sh +dox repl.1

description: Histone H1.5 depletion by RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.5 shRNA expression vector (pLVTHM) induced by doxycyclin


title: H1.4 sh +dox repl.2

description: Histone H1.4 depletion by RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.4 shRNA expression vector (pLVTHM) induced by doxycyclin

source_name: Histone H1.4 shRNA vector; induced by doxycyclin treatment

tag: Histone H1.4 depletion

tag: Histone H1.4 shRNA vector


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC12_b7_s5


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC27_CGHb14_s28


title: Uterine cervix normal ectocervix VUMC_ectocervix_b7_s52

description: pool of RNA isolated from 3 histologically normal cervical biopsies

tag: normal ectocervix


title: H1.3 sh +dox repl.1

description: Histone H1.3 depletion by RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.3 shRNA expression vector (pLVTHM) induced by doxycyclin

source_name: Histone H1.3 shRNA vector; induced by doxycyclin treatment

tag: Histone H1.3 depletion

tag: Histone H1.3 shRNA vector


title: H1.4 sh +dox repl.1

description: Histone H1.4 depletion by RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.4 shRNA expression vector (pLVTHM) induced by doxycyclin


title: H1.4 sh -dox repl.2

description: Negative control for histone H1.4 RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.4 shRNA expression vector (pLVTHM) uninduced

source_name: Histone H1.4 shRNA vector; uninduced, no doxycyclin treatment


title: H1.3 sh -dox repl.1

description: Negative control for histone H1.3 RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.3 shRNA expression vector (pLVTHM) uninduced

source_name: Histone H1.3 shRNA vector; uninduced, no doxycyclin treatment


title: H1.4 sh -dox repl.1

description: Negative control for histone H1.4 RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.4 shRNA expression vector (pLVTHM) uninduced


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC15_CGHb12_s51

tag: squamous cell carcinoma


title: H1.3 sh -dox repl.2

description: Negative control for histone H1.3 RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.3 shRNA expression vector (pLVTHM) uninduced


title: H1.3 sh +dox repl.2

description: Histone H1.3 depletion by RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.3 shRNA expression vector (pLVTHM) induced by doxycyclin


title: Uterine cervix normal ectocervical epithelium VUMC_ectocervix1_b7_s22

description: pool of normal ectocervical RNA collected by brush from 4 uteri extirpated for benign non-cervical disorders

tag: normal ectocervical epithelium


title: H1.2 sh -dox repl.2

description: Negative control for histone H1.2 RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.2 shRNA expression vector (pLVTHM) uninduced

source_name: Histone H1.2 shRNA vector; uninduced, no doxycyclin treatment

tag: Histone H1.2 shRNA vector


title: H1.0 sh +dox repl.2

description: Histone H1.0 depletion by RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.0 shRNA expression vector (pLVTHM) induced by doxycyclin

source_name: Histone H1.0 shRNA vector; induced by doxycyclin treatment

tag: Histone H1.0 depletion

tag: Histone H1.0 shRNA vector


title: H1.0 sh +dox repl.1

description: Histone H1.0 depletion by RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.0 shRNA expression vector (pLVTHM) induced by doxycyclin

tag: T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC2_CGHb14_s26

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 39 years, contains Human Papilloma Virus type 16

source_name: uterine cervix

tag: Pooled DNA from the blood of 10 normal male individuals


title: gura_sed_fum_BR2A

source_name: Sediment, BR2A

tag: grown to mid-log anaerobically in acetate amended Rifle sediment batch cultures

source_name: Fumarate, BR2A

tag: grown to mid-log anaerobically in batch cultures with acetate as the electron donor and fumarate as the electron acceptor


title: H1.2 sh -dox repl.1

description: Negative control for histone H1.2 RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.2 shRNA expression vector (pLVTHM) uninduced

tag: no depletion


title: H1.0 sh -dox repl.2

description: Negative control for histone H1.0 RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.0 shRNA expression vector (pLVTHM) uninduced

source_name: Histone H1.0 shRNA vector; uninduced, no doxycyclin treatment

tag: uninduced, no doxycyclin treatment


title: Uterine cervix squamous cell carcinoma VUMC_CxSCC12_CGHb15_s43

description: poorly differentiated squamous cell carcinoma of the cervix, patient age 44 years, contains Human Papilloma Virus type 16


title: H1.0 sh -dox repl.1

description: Negative control for histone H1.0 RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.0 shRNA expression vector (pLVTHM) uninduced


title: H1.2 sh +dox repl.2

description: Histone H1.2 depletion by RNAi, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.2 shRNA expression vector (pLVTHM) induced by doxycyclin

source_name: Histone H1.2 shRNA vector; induced by doxycyclin treatment

tag: Histone H1.2 depletion

tag: induced by doxycyclin treatment


title: H1.2 sh +dox repl.1

description: Histone H1.2 depletion by RNAi, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and H1.2 shRNA expression vector (pLVTHM) induced by doxycyclin


title: Uterine cervix normal endocervical epithelium VUMC_endocervix_b7_s20

description: pool of normal endocervical RNA collected by brush from 5 uteri extirpated for benign non-cervical disorders

tag: normal endocervical epithelium

source_name: universal human reference RNA (Stratagene)

tag: Pooled RNA of 10 cell lines giving broad gene coverage


title: Uterine cervix adenocarcinoma VUMC_CxAdCA12_CGHb14_s65

description: moderately differentiated adenocarcinoma of the cervix, patient age 41 years, contains Human Papilloma Virus type 18

tag: adenocarcinoma


title: Uterine cervix adenocarcinoma VUMC_CxAdCA7_b7_s15

description: moderately differentiated adenocarcinoma of the cervix, patient age 31 years, contains Human Papilloma Virus type 16


title: Uterine cervix adenocarcinoma VUMC_CxAdCA12_b7_s21


title: Uterine cervix normal ectocervical epithelium VUMC_ectocervix2_b7_s23


title: Uterine cervix adenocarcinoma VUMC_CxAdCA5(7)_CGHb14_s62


title: Uterine cervix adenocarcinoma VUMC_CxAdCA11_b7_s17

description: moderately differentiated adenocarcinoma of the cervix, patient age 64 years, contains Human Papilloma Virus type 18


title: control +dox repl.2

description: Negative control for transfection and doxycyclin treatment, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM) induced by doxycyclin

source_name: empty shRNA vector; induced by doxycyclin treatment

tag: empty shRNA vector


title: control +dox repl.1

description: Negative control for transfection and doxycyclin treatment, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM) induced by doxycyclin


title: Uterine cervix adenoarcinoma VUMC_CxAdCA1_b7_s14

description: well differentiated adenocarcinoma of the cervix, patient age 34 years, contains Human Papilloma Virus type 16

tag: adenoarcinoma


title: VPJT07-R

status: Public on Oct 19 2008

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

description: this sample is matched to VPJT07-C

hyb_protocol: As recommended by Agilent

scan_protocol: Agilent DNA microarray scanner and Feature Extraction Software with default settings for oligonucleotide expression arrays were used to capture and process array images.

data_processing: Following hybridization, slides are washed, scanned and quantitated with the Axon GenePix 4000 microarray reader (Axon Instruments). Gene expression results are analyzed using GeneSpring (Silicon Genetics) software. Intensity dependent normalization is applied, where the ratio is reduced to the residual Lowess fit of the intensity versus ratio curve. The measured intensity of each gene is divided by its reference channel (signal from the universal reference RNA) in each sample. When the reference channel is below 10, the data point is considered uninformative. The ratios (sample over reference) for the tumor core experiments and invasive rim experiments are averaged and compared. Genes that are more than two-fold differentially regulated in the majority of the matched core/invasive rim sets are selected.

label_protocol: 500 hundred nanograms of total RNA from each sample (either rim or core) and human universal reference RNA (Stratagene, La Jolla, CA) underwent one round of linear amplification in RiboAmp RNA Amplification kit. Sample cDNA was labeled with Cyanine 5 (Cy5) while reference RNA was labeled with Cyanine 3(Cy3) - CTP (PerkinElmer, Boston, MA) and cDNA concentration was assessed spectro-photometrically (GeneQuant II, Bottom Ltd., Cambridge, UK). Any remaining unamplified sample RNA was saved for validation studies.

extract_protocol: Tumors are embedded in OCT, then sectioned in a cryostat at -20C, to a thickness of 8-10 um and placed onto HistoGene slides. Sections to be microdissected are removed from the -80C fixed and stained with an abbreviated Hematoxylin and Eosin protocol. Two thousand tumor core and invasive cells are dissected onto separate caps using the PixCell II instrument using CapSure™ Macro LCM Caps. The CapSure™ Macro LCM Caps LCM 0211 should be used with the AutoPix instrument. Cells in the tumor core are identified by nuclear atypia and size and captured using the larger spot sizes. Tumor cells immediately adjacent to necrotic areas, cortical areas, cells with small regular nuclei, endothelial and blood cells should be avoided. Individual white matter invading GBM cells can be identified by means of their nuclear atypia and heteropyknotic staining, which is consistent with that of the cells within the tumor core. They should be microdissected using the 7.5 um laser spot size and the initial power settings recommended by the PixCell II manual. After microdissection all harvested material should immediately be lysed on the cap by applying the lysis buffer (XB) from the PicoPure RNA Isolation Kit according to the PicoPure protocol and stored -80C. Cell populations harvested on different caps can be pooled at the time of RNA isolation. RNA integrity is varified by identification of distinct 28S and 18S ribosomal bands with an Agilent Bioanalyzer using the RNA 6000 Nano LabChip kit. Total RNA was isolated from 2000 LCM cells (to ensure at least 10 ng total RNA) using the PicoPure RNA solation Kit, following manufacturers protocol. mRNA is reverse transcribed with the RiboAmp RNA Amplification kit.

tag: cells captured from the rim of the GBM labeled VPJT07

source_name: Human Universal Reference RNA

extract_protocol: sample ordered from Stratagene as purified reference RNA

tag: Human Universal Reference RNA from Stratagene


title: VPJT03-C

description: this sample is matched to VPJT03-R

tag: Cells captured from the core of the GBM labeled VPJT03


title: Uterine cervix adenocarcinoma VUMC_CxAdCA10_CGHb15_s41

description: moderately differentiated adenocarcinoma of the cervix, patient age 39 years, contains Human Papilloma Virus type 16

source_name: Reference DNA


title: VPJT01-C

description: this sample is matched to VPJT01-R

tag: Cells captured from the core of the GBM labeled VPJT01


title: TB197-R

description: this sample is matched to TB197-C

tag: Cells captured from the Rim of the GBM TB197


title: VPJT03-R

description: this sample is matched to VPJT03-C

tag: Cells captured from the rim of the GBM labeled VPJT03


title: TB197-C

description: this sample is matched to TB197-R

tag: cells captured from the core of the GBM labeled TB197


title: VPJT07-C

description: this sample is matched to VPJT07-R

tag: Cells captured from the core of the GBM labeled VPJT07


title: Uterine cervix adenocarcinoma VUMC_CxAdCA11_CGHb15_s42

tag: Pooled DNA from the blood of 10 normal male individuals


title: TB195-C

description: this sample is matched to TB195-R

tag: Cells captured from the core of the GBM tumor labeled TB195


title: TB195-R

description: this sample is matched to TB195-C

tag: Cells captured from the rim of the GBM labeled TB195


title: Uterine cervix adenocarcinoma VUMC_CxAdCA1_CGHb15_s39


title: VPJT01-R

description: this sample is matched to VPJT01-C

tag: cells captured from the rim of the GBM labeled VPJT01


title: TB186-C

description: this sample is matched to TB186-R

tag: Cells captured from the core of the GBM labeled TB186

tag: sample ordered from Stratagene as purified reference RNA


title: TB186-R

description: this sample is matched to TB186-C

tag: Cells captured from the rim of the GBM labeled TB186


title: TB187-R

description: this sample is matched to TB187-C

tag: Cells captured from the Rim of the GBM labeled TB187


title: BTTB965-R

description: this sample is matched to BTTB965-C

tag: Cells captured from the rim of the GBM labeled BTTB965


title: Uterine cervix adenocarcinoma VUMC_CxAdCA10_b7_s16

tag: adenocarcinoma

tag: Pooled RNA of 10 cell lines giving broad gene coverage


title: BTTB1020-C

description: this sample is matched to BTTB1020-R

tag: Cells captured from the core of the GBM labeled BTTB1020

tag: Human Universal Reference RNA from Stratagene


title: BTTB965-C

description: this sample is matched to BTTB965-R

tag: Cells captured from the core of the GBM labeled BTTB965


title: BNI-839-R

description: this sample is matched to BNI-839-C

source_name: BNI-839 rim

tag: Cells captured from the rim of the GBM sample labeled BNI-839


title: BNI-9076-R

description: this sample is matched to BNI-9076-C

source_name: BNI-9076 rim

tag: Cells captured form the Rim of the GBM sample labeled BNI-9076


title: BNI-9065-R

description: this sample is matched to BNI-9065-C

source_name: BNI-9065 rim

tag: Cells captured from the Rim of the GBM sample BNI-9065.


title: BTTB1020-R

description: this sample is matched to BTTB1020-C

tag: Cells captured from the rim of the GBM labeled BTTB1020


title: BNI-9076-C

description: this sample is matched to BNI-9076-R

source_name: BNI-9076 core

tag: Cells captured from the core of the GBM sample labeled BNI-9076


title: BTTB886-C

description: this sample is matched to BTTB886-R

tag: Cells captured from the core of the GBM labeled BTTB886


title: TB187-C

description: this sample is matched to TB187-R

tag: Cells captured from the core of the GBM labeled TB187


title: BTTB886-R

description: this sample is matched to BTTB886-C

tag: Cells captured from the rim of the GBM labeled BTTB886


title: BNI-9065-C

description: this sample is matched to BNI-9065-R

source_name: BNI-9065 core

tag: Cells captured from the core of the GBM sample labeled BNI-9065


title: BNI-839-C

description: this sample is matched to BNI-839-R

source_name: BNI-839 core

tag: Cells captured from the core of the GBM labeled BNI-839


title: BNI-758-R

description: this sample is matched to BNI-758-C

source_name: BNI-758 rim

tag: Cells captured from the Rim of the GBM sample labeled BNI-758


title: BNI-660-C

description: this sample is matched to BNI-660-R

source_name: BNI-660 core

tag: Cells captured from the Core of GBM labeled BNI-660


title: BNI-370-C

description: this sample is matched to BNI-370-R

source_name: BNI-370 core

tag: Cells captured from the core of the GBM tumor labeled BNI-370


title: BNI-758-C

description: this sample is matched to BNI-758-R

source_name: BNI-758 core

tag: Cells captured from the core of the GBM labeled BNI-758


title: BNI-660_R

description: this sample is matched to BNI-660-C

source_name: BNI-660 rim

tag: Cells captured from the Rim of the GBM labeled BNI-660


title: Hypothalamus, Chick fasted 48h, fed 48h, Replicate 3

status: Public on Oct 18 2008

city: College Park

first: Tom

middle: E.

last: Porter

state: MD

address: Building 142

department: Animal and Avian Sciences

institute: University of Maryland

description: Biological Replicate 3 of 4.

hyb_protocol: The arrays were baked at 90C for 90 minutes prior to use.  Pre-treatment of slides was accomplished by incubation of slides in pre-hybridization solution (5xSSC, 0.1%SDS, and 1% BSA) for 45 min at 42C.  Then slides were dipped in 2x SSC and 0.2x SSC for 5 min each.  Slides were dried by centrifugation (5 min at 1000 x g).  An aliquot of 5 µg of labeled, purified aRNA was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70C.  Stop solution was added to terminate the reaction, and samples were dried again in the SpeedVac.  Pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN) was used to reconstitute the samples in a 30 µL volume.  Reference aRNA samples used within the same day were pooled and aliquoted. One reference pool (30 µL) and one sample (target) (30 µL) were mixed and 2.5 µL of 10mg/mL yeast tRNA and 2.5 µL of 10mg/mL salmon testes DNA (Sigma, St. Louis, MO) were added. The target/reference mixture (65 µL) was heated to 94C for 2 min for denaturation, cooled at room temperature, and loaded to the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA), which was overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). Slides were then incubated for 14-16h  at 42C inside a light-tight sealed box in a water bath.  Following incubation, the cover slip was removed by flushing with wash solution #1 (1x SSC, 0.2% SDS, 0.5% DTT).   Sequential washes were as follows: Ten min at 42C in pre-warmed wash solution #1, five min at room temp in wash solution #2 (0.1x SSC, 0.2% SDS, 0.5% DTT), and one min at room temperature in wash solution #3 (0.1x SSC, 0.5% DTT).  Slides were then washed with ddH2O and dried by centrifugation.  Slides were stored in 50 mL conical tubes covered in foil in the presence of nitrogen gas until scanning.

scan_protocol: GenePix 4000B microarray scanner was used to scan each slide. The image was acquired at 10 µm resolution during simultaneous scanning of two wavelengths, 532nm (green) and 635nm (red).  The PMT count ratio was adjusted to 1 during preview at low resolution scanning, and a high resolution TIFF image file was then obtained.

data_processing: Each TIFF image was further analyzed with GenePix Pro software, generating a GenePix Report (gpr) file.  GenePix report files were converted to .mev files using Express Converter software freely available from The Institute for Genomic Research (TIGR) website.  Converted files were Lowess normalized using Microarray Data Analysis System (MIDAS) software, also freely available on the TIGR website.

label: Alexa 555

organism: Gallus gallus

source_name: Hypothalami, fasted for 48h, fed for 48h

label_protocol: Dye labeling was accomplished according to the instructions for dye labeling and labeled aRNA cleanup with the Amino Allyl MessageAmpTM II aRNA Amplification Kit.  Twenty micrograms of aRNA were dried to a minimal volume (not overdryed) in a SpeedVac concentrator. The aRNA was then reconstituted in 9µL of coupling buffer and mixed with 11µL of prepared dye (Alexa fluor 555 carboxylic acid, succinimidyl ester and Alexa fluor 647 carboxylic acid, succinimidyl ester (Invitrogen, Eugene, OR)). Aliquots of the dye (60 µg) were dissolved in DMSO just prior to use.  aRNA with dye was incubated in the dark for one h at room temperature for coupling.  The incorporation of dye and concentration of aRNA were quantified with the NanoDrop spectrophotometer (Wilmington, DE) and incorporation efficiency was determined using the calculator available at www.ambion.com/tools/dye.

growth_protocol: Fertile eggs (Ross x Ross) were obtained from Allen’s hatchery (Seaford, DE) and incubated at the University of Maryland under standard conditions. The chicks for this experiment were collected within a four-hour window of hatching, and males were randomly assigned to treatment groups.  All chicks were given free access to water.  Chicks in the ‘Hatch’ group did not receive feed before samples were collected.  Fed chicks received standard chick starter ration ad libitum, and all chicks were brooded at age appropriate temperatures in battery brooders.

extract_protocol: Total RNA was isolated from hypothalami using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol.  The isolated RNA was quantified using the Ribogreen RNA Quantitation Kit (Molecular Probes, Eugene, OR) and RNA quality was determined using a Bioanalyzer 2100 (Agilent, Wilmington, DE).  RNA was then amplified using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, TX).  One round of RNA amplification was performed using 4µg of total RNA.  In vitro transcription (IVT) was performed for 14h at 37C.  aRNA was quantified and analyzed for quality using the same methods as were used for total RNA.

treatment_protocol: Feed access (fed or fasted) was administered according to the individual sample descriptions.  At the time of sampling, chicks were killed and the hypothalami were immediately removed and snap frozen in liquid nitrogen.  Samples were stored at -80C until RNA extraction.

tag: Fasted 48h, fed 48h

tag: Age

tag: Pool of 4 hypothalami

label: Alexa 647

source_name: Hypothalami, reference pool

tag: Pool of 160 hypothalami

tag: Pool of all samples in experiment


title: BNI-364-R

description: this sample is matched to BNI-364-C

source_name: BNI-364 rim

tag: Cells captured from the RIM of a GBM tumor labeled BNI-364

tag: Human Universal Reference RNA from Stratagene


title: Hypothalamus, Chick fasted 48h, fed 48h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fasted 48h, fed 48h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fasted 48h, fed 48h, Replicate 2

description: Biological Replicate 2 of 4.


title: BNI-370-R

description: this sample is matched to BNI-370-C

source_name: BNI-370 rim

tag: Cells captured from the rim of the GBM tumor from the sample labeled BNI-370


title: 49JAP-R

description: this sample is matched to JAP49-C

source_name: 49JAP rim

tag: Rim cells captured from the GBM labeled 49JAP

source_name: Human Universal Reference RNA


title: 44JAP-C

description: This sample is matched to 44jap_rim

source_name: 44JAP core

tag: GBM tumor label 44JAP

extract_protocol: sample order from Stratagene as purified reference RNA


title: BNI-364-C

description: this sample is matched to BNI-364-R

source_name: BNI-364 core

tag: Cells from the core of the GBM sample labeled BNI-364


title: 44JAP-R

description: this sampple is matched to JAP44-C

source_name: JAP44 rim

tag: Cells captured from the rim of GBM tumor labeled 44JAP


title: 49JAP-C

description: this sample is matched to JAP49-R

source_name: 49JAP core

tag: Cells captured from the core of the GBM tumor labeled 49JAP


title: Hypothalamus, Chick fed 96h, Replicate 4

description: Biological Replicate 4 of 4.

source_name: Hypothalami, fed for 96h

tag: Fed for 96h


title: Hypothalamus, Chick fed 96h, Replicate 3

description: Biological Replicate 3 of 4.


title: Hypothalamus, Chick fasted 48h, fed 24h, Replicate 4

description: Biological Replicate 4 of 4.

source_name: Hypothalami, fasted for 48h, fed for 24h

tag: Fasted 48h, then fed 24h


title: Hypothalamus, Chick fed 96h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Chick fasted 48h, fed 24h, Replicate 3

description: Biological Replicate 3 of 4.


title: Hypothalamus, Chick fasted 48h, fed 24h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Chick fasted 48h, fed 24h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fed for 72h, Replicate 3

description: Biological Replicate 3 of 4.

source_name: Hypothalami, fed for 72h

tag: Fed for 72h


title: Hypothalamus, Chick fed 96h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fed for 72h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fasted 48h, fed 4h, Replicate 2

description: Biological Replicate 2 of 4.

source_name: Hypothalami, fasted for 48h, fed for 4h

tag: Fasted 48h, then fed 4h


title: Hypothalamus, Chick fasted 48h, fed 4h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fed for 72h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Chick fed for 72h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fasted 48h, fed 4h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fasted 48h, Replicate 4

description: Biological Replicate 4 of 4.

source_name: Hypothalami, fasted for 48h

tag: Fasted for 48h


title: Hypothalamus, Chick fasted 48h, Replicate 3

description: Biological Replicate 3 of 4.

tag: Age


title: Hypothalamus, Chick fasted 48h, fed 4h, Replicate 3

description: Biological Replicate 3 of 4.

tag: Pool of 4 hypothalami


title: Hypothalamus, Chick fasted 24h, Replicate 1

description: Biological Replicate 1 of 4.

source_name: Hypothalami, fasted for 24h

tag: Fasted for 24h

tag: Pool of 160 hypothalami


title: Hypothalamus, Chick fed for 48h, Replicate 1

description: Biological Replicate 1 of 4.

source_name: Hypothalami, fed for 48h

tag: Fed for 48h

tag: Pool of all samples in experiment


title: Hypothalamus, Chick fasted 24h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Chick fed for 48h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fasted 24h, Replicate 3

description: Biological Replicate 3 of 4.


title: Hypothalamus, Chick fasted 24h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fed for 48h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Chick fed for 48h, Replicate 3

description: Biological Replicate 3 of 4.


title: Renal Clear Cell Carcinoma_010412

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

description: Gene expression data from Human RCC sample

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. UNC Microarry Database software was used.

source_name: mRNA from Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core

growth_protocol: Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility

extract_protocol:
Quality Control: RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell histopathology
RNA was extracted with Qiagen RNeasy kit.

tag: Organism Part

value: Kidney

tag: Disease State

value: Clear Cell Carcinoma

tag: BioSourceType

value: Frozen Sample

tag: BioSource Provider

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: Renal Clear Cell Carcinoma_047023


title: Hypothalamus, Chick fed for 24h, Replicate 3

description: Biological Replicate 3 of 4.

source_name: Hypothalami, fed for 24h

tag: Fed for 24h

source_name: Hypothalami, reference pool


title: Hypothalamus, Chick fasted 48h, Replicate 2

description: Biological Replicate 2 of 4.


title: Renal Clear Cell Carcinoma_020139


title: Hypothalamus, Chick fed for 24h, Replicate 4

description: Biological Replicate 4 of 4.


title: Hypothalamus, Chick fed for 24h, Replicate 1

description: Biological Replicate 1 of 4.


title: Hypothalamus, Chick fed for 24h, Replicate 2

description: Biological Replicate 2 of 4.


title: Hypothalamus, Day-of-hatch chick, Replicate 3

description: Biological Replicate 3 of 4; Control.

source_name: Hypothalami, day of hatch

tag: No treatment


title: Renal Clear Cell Carcinoma_010392


title: Renal Clear Cell Carcinoma_037070


title: Renal Clear Cell Carcinoma_010111


title: Renal Clear Cell Carcinoma_010106


title: Renal Clear Cell Carcinoma_010105


title: Hypothalamus, Day-of-hatch chick, Replicate 2

description: Biological Replicate 2 of 4; Control.


title: Renal Clear Cell Carcinoma_950009


title: Renal Clear Cell Carcinoma_010397


title: Renal Clear Cell Carcinoma_970053


title: Hypothalamus, Day-of-hatch chick, Replicate 4

description: Biological Replicate 4 of 4; Control.


title: Right un-irradiated

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

country: Japan

institute: AIST

description:
Keyword = rat
Keyword = irradiation

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

organism: Rattus norvegicus

source_name: RIGHT STRIATUM control_Replication1

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Adult male Wistar rats

extract_protocol: TRIZOL Reagent method

treatment_protocol: Rat striatum at 16 h, control

tag: control, untreated

treatment_protocol: Rat striatum at 16 h post-irradiation, un-irradiated

tag: Un-irradiated


title: Right un-irradiated_2

description:
Keyword = rat
Keyword = irradiation


title: Left irradiated_2

description:
Keyword = rat
Keyword = irradiation

source_name: LEFT STRIATUM control_Replication1

source_name: LEFT STRIATUM irradiated_Replication1

treatment_protocol: Rat striatum at 16 h post-irradiation, irradiated

tag: irradiated, treated


title: Left irradiated

description:
Keyword = rat
Keyword = irradiation


title: Renal Clear Cell Carcinoma_941018


title: S95

status: Public on Oct 17 2008

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

description: Normalized (global median) ratio values obtained for each probe were averaged across replicates. Significant differences were defined as those displaying an average expression fold change greater than 2-fold (log (base 2) ratio ≥ 1.0).

hyb_protocol: Labeled total RNA (1 µg) was hybridized to the microarrays using the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions. Post-hybridization washes were done according to the manufacturer’s (Genisphere) instructions.

scan_protocol: Hybridization signals were measured using a ScanArray Express (PerkinElmer, Boston, MA, USA) and the images where processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA).

data_processing: Normalization of log2 ratios using global median normalization

label: Cy5 Fluor

organism: Ovis aries

source_name: Animal 48

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Cy5 and Cy3 fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

growth_protocol: Lack of B. ovis infection was assessed by culture.

extract_protocol: Total RNA was isolated from Buffy coat samples of experimentally infected and control sheep using TriReagent (Sigma, St. Louis, MO, USA) according to manufacturer’s instructions. The RNA was checked using the Experion™ Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA) to evaluate the quality and integrity of RNA preparations.

tag: Animal 48, 15 days pre vaccination that after challenge resulted infected

label: Cy3 Fluor

source_name: Uninfected animal 45

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

tag: Uninfected animal 45, 15 days pre vaccination that after challenge resulted non infected


title: Laboratory strain RM1221_rep6, Lab Control

city: Lethbridge

first: Eduardo

middle: N

last: Taboada

state: Alberta

address: PO Box 640, TWP Rd. 9-1

country: Canada

institute: Public Health Agency of Canada

description: RM1221 - 05Sep28

hyb_protocol: In a fresh 1.5 ml amber tube, amounts corresponding to 40 pmol of both the reference strain (Cy3) and test strain (Cy5) were combined in a total volume of 20 µl. Labeled targets were prepared by addition of 55µl of SlideHyb Buffer #2 (Ambion, Austin, TX, USA) to the 20 µl volume obtained after the quantification step, mixing gently and heating for 5 min (65-67˚C). Arrays were prepared by submerged in warm prehybridization solution (Genicon Sciences Corporation, now part of Invitrogen, Carlsbad, CA, USA) and incubating for 30 min at 42˚C. Each array was then washed in fresh distilled H2O 10 times and in 100% isopropanol 10 times. Arrays were then dried with filtered air. Denatured targets were then added to the array under a Lifter Slip. Each array was hybridized at 42˚C in a humidified chamber for 18-24 h. After incubation, the Lifter Slips were removed, and the arrays immersed in fresh wash 1 solution (1x sodium chloride-sodium citrate (SSC)/0.1% sodium dodecyl sulfate, 42˚C for 5 min.) This step was then repeated twice. Arrays were then immersed in wash solution 2 (1xSSC) at 42˚C for 5 min (repeated twice), and then in wash solution 3 (0.1xSSC) at 42˚C for 5 min (repeated twice). Slides were then rinsed in warm distilled H2O (42˚C), dried with filtered air, placed into clean slide mailers and protected from direct light until scanned.

scan_protocol: Arrays were scanned using GenePix Pro version 4.1 (GenePix 4000B scanner, MDS Analytical Technologies, Mississauga, ON, Canada) or Jaguar, 2.0 (ArrayScanner 428, Affymetrix Inc, Santa Clara, CA,USA). Cy 3 and Cy 5 were scanned at wavelengths of approximately 532 and 635 respectively, both with 100% power.

data_processing: Primary image analysis was performed with ArrayVision version 8.0, rev. 3.0 (Imaging Research Inc.). The background was then subtracted from the raw spot intensity for both reference and test strain, giving a net intensity for each spot. Prior to all subsequent analyses, anomalous spots resulting from printing errors were removed from the dataset. The average net intensity data in reference and test channels for each ORF on the array was then obtained by averaging the net intensity of remaining replicate spots. Global loess normalization was performed with ArrayPipe (http://www.pathogenomics.ca/arraypipe/). Preliminary analysis of our data set revealed that low intensity data reduced the concordance of data from replicate arrays. A custom script was written in VBA for Microsoft Office Excel to test pixel intensity cut-offs from 200 to 1200 pixel units (in 20 unit increments) while monitoring concordance of replicate data. This analysis allowed us to determine intensity and log ratio cut-offs which would maximize the amount of reliable data retained for subsequent analysis and minimize the adverse effects of low signal data on replicate concordance. ORFs and arrays in which greater than 5% of the data yielded less than 500 pixel units in the reference channel were excluded from subsequent analysis.

organism: Campylobacter jejuni

source_name: genomic DNA from strain Laboratory strain NCTC11168

label_protocol: To perform random priming reaction 9 µg of random primers (Invitrogen Corporation, Carlsbad, CA, USA) were added to approximately 6 µg of genomic C. jejuni DNA in a volume of 40.5 µl, denatured at 95-97˚C for 6 min, and snap cooled on ice. The random priming reaction was set-up by adding 5 microlitres of 10 x Klenow reaction buffer, 1.5 µl Cy labeled dCTP, 1 µl dNTP, and 20 units exonuclease-free Klenow; tubes were incubated at 37˚C for 2h. Cleanup of probes was carried out using the Qiagen MinElute Reaction Cleanup Kit as per manufacturer’s specifications with a final elution volume of 13 µl distilled H2O. Labeled DNA and dye incorporation efficiency was quantified using a spectrophotometer (Ultrospec® 3000, Pharmacia Biotech) and equivalent Cy3 (control) and Cy5 (tester) molarities were used in each hybridization.

growth_protocol: Isolates were plated onto Mueller-Hinton (MH) agar for 48 hours at 43°C to ensure pure culture, and then streaked onto three MH plates and incubated for 16-18 hours at 37°C (10%CO2, 5% O2, 85% N2). Growth from three plates per strain was then suspended in a 50% brain-heart infusion-25% glycerol mixture and frozen to -70C for genotyping at a later date. Prior to DNA isolation, glycerol stocks were used to grow a confluent lawn on an M-H plate and grown as described above.

extract_protocol: Genomic DNA isolation was done using a modification of the hexadecyktrimethyl ammonium bromide (CTAB) procedure (Current Protocols in Molecular Biology section 2.4.2). Briefly, cells were suspended in 567 µL of TE (10mM Tris HCl and 1 mM EDTA pH 8.0).  Proteinase K and sodium dodecyl sulfate were added to a final concentration of 100 µg/mL and 0.5% respectively. After incubation for 1 h at 37οC 100 µL of 5 M NaCl was added and the suspension was mixed thoroughly. 80 µL of 10% CTAB in 0.7 M NaCl the solution added and the mixture was incubated at 65 οC for 10 min. An equal volume of chloroform/isoamyl alcohol (24:1) was added and after thorough mixing the CTAB-protein/polysaccharide complex was removed by centrifugation. The aqueous supernatant was transferred to a fresh tube and the remaining protein was extracted with phenol/chloroform/isoamyl alcohol (25:24:1). The supernatant was precipitated with 0.6 volumes of isopropanol and the precipitate was dissolved in 250 µL of water.

treatment_protocol: No treatment

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Laboratory strain RM1221

tag: C. jejuni Laboratory strain RM1221, Lab Control


title: S96

source_name: Animal 54

tag: Animal 54, 15 days pre vaccination that after challenge resulted infected

source_name: Uninfected animal 47

treatment_protocol: Lack of B. ovis infection was assessed by culture.

tag: Uninfected animal 47, 15 days pre vaccination that after challenge resulted non infected


title: S94

source_name: Animal 44

tag: Animal 44, 15 days pre vaccination that after challenge resulted infected

source_name: Uninfected animal 42

tag: Uninfected animal 42, 15 days pre vaccination that after challenge resulted non infected


title: S89

source_name: Infected animal 48, 60 days post infection and 235 days post vaccination

growth_protocol: The rams were challenged with a total dose of 1.7 x 109 B. ovis CFU, as shown by viable cell counts made on the day of inoculation, in 60 microliters doses (30 microliters administered conjunctivally and 30 microliters intrapreputially).

extract_protocol: Total RNA was isolated from Buffy coat samples of experimentally infected and control sheep using TriReagent (Sigma, St. Louis, MO, USA) according to manufacturer’s instructions. The RNA was checked using the Experion™ Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA) to evaluate the quality and integrity of RNA preparations

treatment_protocol: For vaccination, animals were inoculated with the B. melitensis Rev 1 vaccine strain

tag: Infected animal 48

source_name: Uninfected animal 45 , 60 days post infection and 235 days post vaccination

tag: Uninfected animal 45


title: Hypothalamus, Day-of-hatch chick, Replicate 1

description: Biological Replicate 1 of 4; Control.

tag: Age

tag: Pool of 4 hypothalami

tag: Pool of 160 hypothalami

tag: Pool of all samples in experiment


title: S93

source_name: Animal 54, 15 days pre infection and 190 days post vaccination

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Cy5 and Cy3 fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions

tag: Animal 54 vaccinated that resulted infected after challenge with B. ovis

source_name: Uninfected animal 47, 15 days post infection and 190 days post vaccination

tag: Uninfected animal 47


title: Laboratory strain NCTC11168_rep6, Lab Control

description: NTCT11168 - 06Sep20

tag: C. jejuni Laboratory strain NCTC11168, Lab Control


title: Laboratory strain RM1221_rep1, Lab Control

description: RM1221 - 01Sep28


title: Laboratory strain RM1221_rep3, Lab Control

description: RM1221 - 03Oct21


title: Laboratory strain RM1221_rep4, Lab Control

description: RM1221 - 03Sep28


title: Laboratory strain RM1221_rep5, Lab Control

description: RM1221 - 04Sep28


title: Laboratory strain NCTC11168_rep4, Lab Control

description: NTCT11168 - 04Sep20


title: Laboratory strain NCTC11168_rep3, Lab Control

description: NTCT11168 - 03Sep20


title: S90

source_name: Infected animal 54, 60 days post infection and 235 days post vaccination

tag: Infected animal 54

source_name: Uninfected animal 47 , 60 days post infection and 235 days post vaccination


title: Hypothalamus, Chick fasted 48h, Replicate 1

description: Biological Replicate 1 of 4.

source_name: Hypothalami, fasted for 48h

tag: Fasted for 48h

source_name: Hypothalami, reference pool


title: Laboratory strain NCTC11168_rep2, Lab Control

description: NTCT11168 - 02Sep20

tag: C. jejuni Laboratory strain NCTC11168


title: Laboratory strain NCTC11168_rep5, Lab Control

description: NTCT11168 - 05Sep20


title: Laboratory strain RM1221_rep2, Lab Control

description: RM1221 - 02Sep28

tag: C. jejuni Laboratory strain RM1221, Lab Control


title: S88

source_name: Infected animal 44, 60 days post infection and 235 days post vaccination

tag: Infected animal 44

source_name: Uninfected animal 42 , 60 days post infection and 235 days post vaccination

growth_protocol: Lack of B. ovis infection was assessed by culture

treatment_protocol:
The rams were challenged with a total dose of 1.7 x 109 B. ovis CFU, as shown by viable cell counts made on the day of inoculation, in 60
l doses (30 microliters administered conjunctivally and 30 microliters intrapreputially).

tag: Uninfected animal 42


title: Field Isolate 4332_rep1, Bovine

description: 4332 - 16Sep25

source_name: genomic DNA from strain Field Isolate 4332

tag: C. jejuni Field Isolate 4332, Bovine


title: Field Isolate 4450_rep1, Bovine

description: 4450 - 03Apr24

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4450

tag: C. jejuni Field Isolate 4450, Bovine


title: S91

source_name: Animal 44, 15 days pre infection and 190 days post vaccination

tag: Animal 44 vaccinated that resulted infected after challenge with B. ovis

source_name: Uninfected animal 42 , 15 days post infection and 190 days post vaccination


title: Field Isolate 4427_rep1, Bovine

description: 4427 - 08Apr05

source_name: genomic DNA from strain Field Isolate 4427

tag: C. jejuni Field Isolate 4427, Bovine


title: Field Isolate 4413_rep1, Bovine

description: 4413 - 20Apr10

source_name: genomic DNA from strain Field Isolate 4413

tag: C. jejuni Field Isolate 4413, Bovine


title: Field Isolate 4330_rep1, Bovine

description: 4330 - 20Apr24

source_name: genomic DNA from strain Field Isolate 4330

tag: C. jejuni Field Isolate 4330, Bovine


title: Laboratory strain NCTC11168_rep1, Lab Control

description: NTCT11168 - 01Sep20


title: S92

source_name: Animal 48, 15 days pre infection and 190 days post vaccination

tag: Animal 48 vaccinated that resulted infected after challenge with B. ovis

source_name: Uninfected animal 45 , 15 days post infection and 190 days post vaccination

tag: Uninfected animal 45


title: Field Isolate 4200_rep2, Human Clinical

description: 4200 - 15Sep25

source_name: genomic DNA from strain Field Isolate 4200

tag: C. jejuni Field Isolate 4200, Human Clinical


title: Field Isolate 4200_rep1, Human Clinical

description: 4200 - 04Mar16


title: Field Isolate 4198_rep1, Human Clinical

description: 4198 - 03Sep14

source_name: genomic DNA from strain Field Isolate 4198

tag: C. jejuni Field Isolate 4198, Human Clinical


title: Field Isolate 4197_rep2, Human Clinical

description: 4197 - 14Apr05

source_name: genomic DNA from strain Field Isolate 4197

tag: C. jejuni Field Isolate 4197, Human Clinical


title: Field Isolate 4199_rep1, Human Clinical

description: 4199 - 15Apr05

source_name: genomic DNA from strain Field Isolate 4199

tag: C. jejuni Field Isolate 4199, Human Clinical


title: Field Isolate 4188_rep1, Human Clinical

description: 4188 - 04Sep25

source_name: genomic DNA from strain Field Isolate 4188

tag: C. jejuni Field Isolate 4188, Human Clinical


title: Field Isolate 4151_rep1, Human Clinical

description: 4151 - 01Oct21

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4151

tag: C. jejuni Field Isolate 4151, Human Clinical


title: Field Isolate 4177_rep1, Human Clinical

description: 4177 - 07Sep20

source_name: genomic DNA from strain Field Isolate 4177

tag: C. jejuni Field Isolate 4177, Human Clinical


title: Field Isolate 4153_rep1, Human Clinical

description: 4153 - 07Oct18

source_name: genomic DNA from strain Field Isolate 4153

tag: C. jejuni Field Isolate 4153, Human Clinical


title: Field Isolate 4142_rep2, Human Clinical

description: 4142 - 11Sep25

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4142

tag: C. jejuni Field Isolate 4142, Human Clinical


title: Field Isolate 4142_rep1, Human Clinical

description: 4142 - 10Sep20


title: Field Isolate 4144_rep1, Human Clinical

description: 4144 - 10Apr24

source_name: genomic DNA from strain Field Isolate 4144

tag: C. jejuni Field Isolate 4144, Human Clinical


title: Field Isolate 4143_rep1, Human Clinical

description: 4143 - 09Apr24

source_name: genomic DNA from strain Field Isolate 4143

tag: C. jejuni Field Isolate 4143, Human Clinical


title: Field Isolate 4163_rep2, Human Clinical

description: 4163 - 19Sep25

source_name: genomic DNA from strain Field Isolate 4163

tag: C. jejuni Field Isolate 4163, Human Clinical


title: Field Isolate 4147_rep1, Human Clinical

description: 4147 - 06Oct18

source_name: genomic DNA from strain Field Isolate 4147

tag: C. jejuni Field Isolate 4147, Human Clinical


title: Field Isolate 4145_rep1, Human Clinical

description: 4145 - 07Sep28

source_name: genomic DNA from strain Field Isolate 4145

tag: C. jejuni Field Isolate 4145, Human Clinical


title: Field Isolate 4158_rep1, Human Clinical

description: 4158 - 18Apr05

source_name: genomic DNA from strain Field Isolate 4158

tag: C. jejuni Field Isolate 4158, Human Clinical


title: Field Isolate 4163_rep1, Human Clinical

description: 4163 - 11Sep20


title: Field Isolate 4153_rep2, Human Clinical

description: 4153 - 14Sep25


title: Field Isolate 4186_rep2, Human Clinical

description: 4186 - 12Sep20

source_name: genomic DNA from strain Field Isolate 4186

tag: C. jejuni Field Isolate 4186, Human Clinical


title: Field Isolate 4149_rep1, Human Clinical

description: 4149 - 16Apr10

source_name: genomic DNA from strain Field Isolate 4149

tag: C. jejuni Field Isolate 4149, Human Clinical


title: Field Isolate 4176_rep1, Human Clinical

description: 4176 - 13Apr02

source_name: genomic DNA from strain Field Isolate 4176

tag: C. jejuni Field Isolate 4176, Human Clinical


title: Field Isolate 4186_rep1, Human Clinical

description: 4186 - 07Sep22


title: Field Isolate 4188_rep2, Human Clinical

description: 4188 - 14Apr24


title: Field Isolate 4189_rep1, Human Clinical

description: 4189 - 06Apr10

source_name: genomic DNA from strain Field Isolate 4189

tag: C. jejuni Field Isolate 4189, Human Clinical


title: Field Isolate 4194_rep1, Human Clinical

description: 4194 - 07Mar30

source_name: genomic DNA from strain Field Isolate 4194

tag: C. jejuni Field Isolate 4194, Human Clinical


title: Field Isolate 4193_rep1, Human Clinical

description: 4193 - 11Apr10

source_name: genomic DNA from strain Field Isolate 4193

tag: C. jejuni Field Isolate 4193, Human Clinical


title: Field Isolate 4190_rep1, Human Clinical

description: 4190 - 10Apr10

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4190

tag: C. jejuni Field Isolate 4190, Human Clinical


title: Field Isolate 4195_rep1, Human Clinical

description: 4195 - 19Apr05

source_name: genomic DNA from strain Field Isolate 4195

tag: C. jejuni Field Isolate 4195, Human Clinical


title: Field Isolate 4197_rep1, Human Clinical

description: 4197 - 08Sep28

source_name: genomic DNA from strain Field Isolate 4197

tag: C. jejuni Field Isolate 4197, Human Clinical


title: Field Isolate 4196_rep1, Human Clinical

description: 4196 - 15Apr24

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4196

tag: C. jejuni Field Isolate 4196, Human Clinical


title: Field Isolate 4141_rep1, Human Clinical

description: 4141 - 15Apr10

source_name: genomic DNA from strain Field Isolate 4141

tag: C. jejuni Field Isolate 4141, Human Clinical


title: Field Isolate 4167_rep1, Human Clinical

description: 4167 - 08Sep20

source_name: genomic DNA from strain Field Isolate 4167

tag: C. jejuni Field Isolate 4167, Human Clinical


title: Field Isolate 4173_rep1, Human Clinical

description: 4173 - 12Sep28

source_name: genomic DNA from strain Field Isolate 4173

tag: C. jejuni Field Isolate 4173, Human Clinical


title: Field Isolate 4170_rep2, Human Clinical

description: 4170 - 06Apr22

source_name: genomic DNA from strain Field Isolate 4170

tag: C. jejuni Field Isolate 4170, Human Clinical


title: Field Isolate 4170_rep1, Human Clinical

description: 4170 - 03Oct18


title: Field Isolate 4134_rep1, Human Clinical

description: 4134 - 15Sep22

source_name: genomic DNA from strain Field Isolate 4134

tag: C. jejuni Field Isolate 4134, Human Clinical


title: Field Isolate 4129_rep1, Human Clinical

description: 4129 - 14Sep20

source_name: genomic DNA from strain Field Isolate 4129

tag: C. jejuni Field Isolate 4129, Human Clinical


title: Field Isolate 4132_rep1, Human Clinical

description: 4132 - 06Apr24

source_name: genomic DNA from strain Field Isolate 4132

tag: C. jejuni Field Isolate 4132, Human Clinical


title: Field Isolate 4122_rep2, Human Clinical

description: 4122 - 08Oct18

source_name: genomic DNA from strain Field Isolate 4122

tag: C. jejuni Field Isolate 4122, Human Clinical


title: Field Isolate 2409_rep2, Bovine

description: 2409 - 17Apr10

source_name: genomic DNA from strain Field Isolate 2409

tag: C. jejuni Field Isolate 2409, Bovine


title: Field Isolate 2515_rep1, Bovine

description: 2515 - 02Apr05

source_name: genomic DNA from strain Field Isolate 2515

tag: C. jejuni Field Isolate 2515, Bovine


title: Field Isolate 2497_rep1, Bovine

description: 2497 - 02Mar28

source_name: genomic DNA from strain Field Isolate 2497

tag: C. jejuni Field Isolate 2497, Bovine


title: Field Isolate 2548_rep1, Bovine

description: 2548 - 02Apr02

source_name: genomic DNA from strain Field Isolate 2548

tag: C. jejuni Field Isolate 2548, Bovine


title: Field Isolate 2650_rep1, Bovine

description: 2650 - 04Apr05

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 2650

tag: C. jejuni Field Isolate 2650, Bovine


title: Field Isolate 2409_rep1, Bovine

description: 2409 - 14Sep22


title: Field Isolate 4136_rep1, Human Clinical

description: 4136 - 07Apr24

source_name: genomic DNA from strain Field Isolate 4136

tag: C. jejuni Field Isolate 4136, Human Clinical


title: Field Isolate 4137_rep1, Human Clinical

description: 4137 - 06Mar30

source_name: genomic DNA from strain Field Isolate 4137

tag: C. jejuni Field Isolate 4137, Human Clinical