title: R. baltica_heat shock_300min_c

description: heat shock 300min vs. reference

source_name: Rhodopirellula baltica heat shock reference

treatment_protocol: In all cases, cells were grown to the OD600nm = 0.5 (corresponding log phase), and an aliquot of cells was collected to serve as the time-zero reference. The culture broth was collected in 500 mL tubes and swirled briefly in an ethanol-dry ice bath to rapidly cool the cultures and "freeze" the RNA profile. Subsequently, the broth was centrifuged at 6000 rpm for 20 min at 4°C (Beckman CoulterTM AvantiTM626 J-20XP, JA10 Rotor). The pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C

label: Alexa 647

source_name: Rhodopirellula baltica, heat shock, 300min

treatment_protocol: Cells grown continuously at 28°C were collected by centrifugation. Aliquots were resuspend in an equal volume of 37°C medium and returned to 37°C for growth. Samples were collected at 10, 20, 40, 60 and 300 min

tag: Heat shock treated for 300min


title: R. baltica_cold shock_20min_b

status: Public on Sep 09 2009

type: RNA

city: Bremen

first: Patricia

last: Wecker

address: Celsiusstr, 1

department: Molecular Ecology

country: Germany

institute: Max Planck Institut for Marine Microbiology

description: cold shock 20min vs. reference

hyb_protocol: Blocking, denaturing, hybridisation, washing and drying of the slides with N2 were carried out in an automated hybridisation station HS400 (Tecan, Crailsheim, Germany). The spotted arrays were blocked in prehybridisation solution containing 250 mM NaCl, 5 mM Tris/HCl at pH 8.0, 50% formamide, 0.5x SSC, 0.05% BSA, and 1% blocking reagent from Roche Diagnostics, Mannheim, Germany for 45 min at 52°C. For hybridisation at least 2 μg of Alexa 546 dye-labelled and 2 μg of Alexa 647 dye-labelled total cDNA were combined and taken up in a final volume of 100 µl DIG Easy Hyb hybridisation solution (Roche Diagnostics, Mannheim, Germany). After the blocking step the sample solution was applied to the arrays, denaturised at 95°C for 3 min and hybridised under stringent conditions at 52°C for over 12 hours. After hybridisation slides were washed at RT in ULTRArray Low Stringency Wash Buffer (Ambion, Austin, USA) and dried by N2.

scan_protocol: Slides were scanned at a resolution of 5 μm using a ScanArray Express Microarray scanner (Perkin Elmer, Wellesley, USA) with varied laser power and sensitivity level of the photomultiplier tube (PMT) for each slide. The provided image analysis software ScanArray Express Version 4.0 was used for automatic spot detection and signal quantification of both fluorophores.

data_processing:
Raw data were automatically processed using the inhouse developed microarray data analysis software tool MADA (www.megx.net/mada). First of all the spot intensities were local background corrected (spot intensity minus spot background intensity). Then signals were only assessed as positive if mean spot pixel intensity was higher than the mean local background intensity plus 2 times the standard deviation of the mean local background pixel intensity. Each gene is spotted in 3 replicates. Spot replicates with poor quality were removed from the data set according to the outlier test of MADA. For this test, first the standard deviation of all replicates is computed. Second, one replicate is omitted and the standard deviation is recalculated, if the deviation differs more than 50% from the previous deviation, the omitted replicate is regarded as outlier. This procedure is alternately repeated for all replicates
The expression is described through the ratio and intensity, where R is the fluorescence log ratio of the experiment time point relative to the control condition (e.g. R = log2 (result of channel 10min / result of channel control/reference)) and I is the log mean fluorescence intensity (e.g. I = log10 (result of channel 10min * result of channel control/reference)).
Each data point represents a regulation factor (ratio) in a logarithmic scale for one gene calculated from the positive replicates for a particular probe coming from two RNA pools (reference and sample). Normalisation was carried out by LOWESS fitting on an R-versus-I plot with a smoothing factor of 0.05. Each time point of the time-series experiment was hybridised independently three times. The expression data (ratio) of the three hybridisations were combined to one expression data point (ratio) by average and the standard deviation was calculated. Only ratios with a standard deviation less than 25% were taken as regulated.
Differentially expressed genes are determinate by a fixed threshold cut off method (i.e. a two-fold increase or decrease) based on the self-self hybridisation.

molecule: total RNA

organism: Rhodopirellula baltica

source_name: Rhodopirellula baltica cold shock reference

label_protocol: cDNA was directly labelled using the PlatinumBrightTM nucleic acid labelling kit based on KREATECH´s patented Universal Linkage System (ULS) (Biocat, Heidelberg, Germany) according to the manufacturer's protocol.

growth_protocol: For all experiments Rhodopirellula baltica SH 1T cells were grown as chemostate cultures in a mineral medium containing 10 mM glucose as sole carbon and 1 mM ammonium chloride as nitrogen source at 28°C (Rabus et al. 2002)

extract_protocol:
The culture pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the proposed protocol of the TRI Reagent® Kit by Ambion (Austin, USA).
cDNA synthesis was performed using the SuperScript direct cDNA labeling system kit by Invitrogen (Karlsruhe, DE) according to the manufacturer´s instructions with random hexamers and unlabeled dCTP/dUTP.

tag: non-treated = reference = time point zero

source_name: Rhodopirellula baltica, cold shock, 20min

treatment_protocol: Cells grown continuously at 28°C were collected by centrifugation. Aliquots were resuspend in an equal volume of 6°C medium and returned to 6°C for growth. Samples were collected at 10, 20, 40, 60 and 300 min

tag: Cold shock treated for 20min

tag: Replicate b


title: R. baltica_cold shock_10min_b

description: cold shock 10min vs. reference

source_name: Rhodopirellula baltica, cold shock, 10min

tag: Cold shock treated for 10min


title: 05-213_NP

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Prostate whole tissue.

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

label: biotin

organism: Homo sapiens

source_name: normal prostate

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

extract_protocol: Prostate tissue total RNA was extracted from the specimen using Rneasy kit (Qiagen).

tag: tissue

value: prostate


title: 05-214_NP

description: Prostate whole tissue.


title: mus-6dpp-5ng_activin-rep2

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

country: USA

institute: Washington State University

description: All methodolgy for this datasets was described in the manuscript of "Developmentally regulated SMAD2 and SMAD3 utilization directs activin signalling outcomes."

hyb_protocol: Standard hybridization protocol using 15ug cRNA wash/stain protocol EukGe-2v5-450

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip® Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis.

data_processing: For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.

label: Biotin

organism: Mus musculus

source_name: Murine 6dpp Sertoli Cell treated with 5ng activin

label_protocol: GeneChip Expression 3' - Amplification one-cycle cDNA synthesis kit (lpn-900431)

extract_protocol: Trizol

tag: Gene expression profile of Sertoli Cell treated with activin


title: mus-15dpp-0ng_activin-rep1

source_name: Murine 15dpp Sertoli Cell treated with 0ng activin


title: mus-6dpp-50ng_activin-rep2

source_name: Murine 6dpp Sertoli Cell treated with 50ng activin


title: 05-213_CaP

description: Prostate cancer whole tissue.

source_name: cancer prostate

tag: gleason

tag: tumor stage

tag: tumor volume


title: 446 | R2Yaa IRF5+/-

type: protein

city: Stanford

first: Chih Long

last: Liu

state: CA

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

institute: Stanford University

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Murine antiserum was probed on the antigen microarray at 1:250 dilution in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20, and incubated for 1.25 hours at 4 degrees Celsius.

scan_protocol: Fluorescent array images were collected for Cy3 with a GenePix 4000B fluorescent scanner at 10 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 6.1 analysis software.

data_processing: After background correction and removal of flagged values, data was normalized by dividing each array value by the goat anti-mouse IgG (25 ug/ml) array feature signal intensity and then multiplying by 10,000 to obtain a normalized signal intensity value.

label: Cy3-conjugated goat anti-mouse antibody

molecule: protein

source_name: Murine antiserum, IRF5+/-

label_protocol: Commercially available Cy3-conjugated goat anti-mouse antibody was added to the microarray at 1:4000 in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20.

extract_protocol: Whole antiserum was obtained.

tag: strain

value: R2Yaa IRF5+/-


title: mus-15dpp-0ng_activin-rep2


title: 445 | R2Yaa IRF5+/-


title: 05-206_CaP

description: Prostate cancer whole tissue.


title: 05-206_NP

description: Prostate whole tissue.


title: 443 | R2Yaa IRF5-/-

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5-/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, IRF5-/-

value: R2Yaa IRF5-/-


title: mus-6dpp-5ng_activin-rep1

description: All methodolgy for this datasetis was described in the manuscript of "Developmentally regulated SMAD2 and SMAD3 utilization directs activin signalling outcomes."


title: R. baltica_heat shock_300min_b

description: heat shock 300min vs. reference

label: Alexa 546

extract_protocol:
The culture pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the proposed protocol of the TRI Reagent® Kit by Ambion (Austin, USA).
cDNA synthesis was performed using the SuperScript direct cDNA labeling system kit by Invitrogen (Karlsruhe, DE) according to the manufacturer's instructions with random hexamers and unlabeled dCTP/dUTP.


title: 05-179_CD26t

description: Prostate cancer cells.

extract_protocol: Prostate tissue was MACS sorted for positive cells.  Total RNA was extracted from the cell lysate using Rneasy kit (Qiagen).

tag: cell type

value: CD26+ MACS sorted cells


title: mus-6dpp-50ng_activin-rep1


title: 442 | R2Yaa IRF5-/-


title: 424 | R2Yaa IRF5-/-


title: 354 | R2Yaa IRF5-/-


title: 423 | R2Yaa IRF5-/-


title: 348 | R2Yaa IRF5+/+

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/+.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, IRF5+/+

value: R2Yaa IRF5+/+


title: mus-6dpp-0ng_activin-rep1

source_name: Murine 6dpp Sertoli Cell treated with 0ng activin


title: R. baltica_heat shock_60min_c

description: heat shock 60min vs. reference

source_name: Rhodopirellula baltica, heat shock, 60min

tag: Heat shock treated for 60min

tag: Replicate c


title: CD49a-1_06-02-04

description: Prostate stromal fibromuscular cells.

value: CD49a+ MACS sorted cells


title: mus-6dpp-0ng_activin-rep2


title: CD49a-4_06-02-04

description: Prostate stromal fibromuscular cells.


title: 328 | R2Yaa IRF5+/+


title: R. baltica_heat shock_60min_a

description: heat shock 60min vs. reference

tag: Replicate a


title: 318 | R2Yaa IRF5+/+


title: R. baltica_heat shock_40min_c

description: heat shock 40min vs. reference

source_name: Rhodopirellula baltica, heat shock, 40min

tag: Heat shock treated for 40min


title: CD49a_03-23-04

description: Prostate stromal fibromuscular cells.


title: R. baltica_heat shock_300min_a

description: heat shock 300min vs. reference


title: 303 | R2Yaa IRF5-/-


title: 317 | R2Yaa IRF5+/+


title: 310 | R2Yaa IRF5-/-


title: R. baltica_heat shock_60min_b

description: heat shock 60min vs. reference


title: R. baltica_heat shock_20min_c

description: heat shock 20min vs. reference

source_name: Rhodopirellula baltica, heat shock, 20min

tag: Heat shock treated for 20min


title: R. baltica_heat shock_20min_b

description: heat shock 20min vs. reference

source_name: Rhodopirellula baltica heat shock reference


title: R. baltica_heat shock_20min_a

description: heat shock 20min vs. reference


title: R. baltica_heat shock_40min_a

description: heat shock 40min vs. reference


title: CD49a_01-26-04

description: Prostate stromal fibromuscular cells.


title: 204 | R2Yaa IRF5-/-


title: 177 | R2Yaa IRF5+/+


title: 227 | R2Yaa IRF5+/-


title: R. baltica_heat shock_reference_c

description: self-self hybridisation (replicate c)


title: R. baltica_heat shock_reference_a

description: self-self hybridisation (replicate a)


title: R. baltica_heat shock_10min_a

description: heat shock 10min vs. reference

source_name: Rhodopirellula baltica, heat shock, 10min

tag: Heat shock treated for 10min


title: R. baltica_heat shock_reference_b

description: self-self hybridisation (replicate b)

tag: non-treated = reference = time point zero


title: R. baltica_heat shock_10min_b

description: heat shock 10min vs. reference


title: WT_toc1-2_LL_CT16

city: Barcelona

first: Paloma

last: Mas

address: C/ Jordi Girona 18-26

department: Genetica Molecular

country: Spain

institute: Consorcio CSIC-IRTA-UAB (CRAG)

description: The control is labeled with Cy3 in the first array (raw data file1) and with Cy5 in the second (raw data file2); toc1-2 is labeled with Cy5 int the first array (raw data file1) and with Cy3 in the second (raw data file2)

hyb_protocol: Performed as previously described (Adie et al., 2007)

data_processing: Raw data was processed with SOLAR (BIOALMA). The data were scaled and normalized with LOWESS procedure (Yang et al., 2002). T statistics and local Z scores were calculated as previously described (Quackenbush et al., 2002).

organism: Arabidopsis thaliana

source_name: Wild-type plants (C24)

growth_protocol: Seedlings were grown on MS3 medium under 12-hour light:12-hour dark (LD) cycles for 10 days followed by two days under constant light conditions

extract_protocol: Total RNA extractions were performed with RNeasy Mini kit (Qiagen)

treatment_protocol: Samples were collected at Circadian Time (CT) 16

tag: ecotype

source_name: TOC1 mutant plants toc1-2 (C24)


title: R. baltica_heat shock_10min_c

description: heat shock 10min vs. reference


title: Huh7_TGFbeta_plus_1

status: Public on Sep 08 2009

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Hepatocellular carcinoma cell lines treated or untreated with TGF-beta.

hyb_protocol: Refer to the Affymetrix Assay System Manual

data_processing: Raw scan data were normalized using rma() function in Bioconductor's affy package (http://www.bioconductor.org/). For the analysis in the manuscript, the normalized signals were further collapsed into gene symbols by taking median values.

source_name: hepatocellular carcinoma cell line

growth_protocol: A human HCC cell line, Huh-7, was obtained from the Riken Bioresource Center (Tsukuba, Japan). The cell line was grown in Dulbecco’s modified Eagle medium (American Type Culture Collection) supplemented with 10% heat-inactivated fetal bovine serum at 37C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from confluent 10cm culture dish using TRIzol reagent (Invitrogen).

treatment_protocol: Cells were treated with TGFbeta (R&D systems) and harvested after 48 hours of incubation.

tag: treated with TGF-beta


title: CD49a_03-04-04

description: Prostate stromal fibromuscular cells.

source_name: normal prostate


title: Huh7_TGFbeta_minus_2

scan_protocol: Refer to the Affymetrix Assay System Manual

tag: untreated with TGF-beta


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion strain replicate 3 dye flip. Slide 10634

city: Seattle

first: Amy

middle: K

last: Schmid

institute: Institute for Systemsbiology

description: vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286

label: Alexa 547

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium sp. NRC-1 wild type.

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm in complex medium (CM).

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium sp. NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).

source_name: Halobacterium sp. NRC-1 ura3 deletion parent strain.

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to stationary phase (OD600 = 1.18)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 1.18.


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion parent strain replicate 3. Slide 10633

description: vs. reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 1.18.

source_name: Halobacterium sp. NRC-1, reference sample


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3. Slide 10683

description: vs. reference

source_name: Halobacterium sp. NRC-1 VNG1451C deletion strain.

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to stationary phase (OD600 = 0.56)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.56.


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion parent strain replicate 3. Slide 10662

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.516)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.516.


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion strain replicate 3 dye flip. Slide 10630

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.724)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.724.


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion parent strain replicate 3. Slide 10629

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.724.


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3. Slide 10631

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.312)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.312.


title: Huh7_TGFbeta_plus_2

label_protocol: Refer to the Affymetrix Assay System Manual


title: Huh7_TGFbeta_minus_1


title: R. baltica_heat shock_40min_b

description: heat shock 40min vs. reference

tag: Replicate b


title: Halobacterium sp. NRC-1 growth curve  in ura3 deletion strain replicate 3 dye flip. Slide 10617

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.516.


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3 dye flip. Slide 10632

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 3 dye flip. Slide 10616

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to early-log phase (OD600 = 0.136)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.136.


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3 dye flip. Slide 10619

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.221)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.221.


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3. Slide 10618

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain replicate 3 dye flip. Slide 10614

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to early-log phase (OD600 = 0.308)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.308.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2 dye flip. Slide 10612

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to stationary phase (OD600 = 0.65)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.65.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain replicate 3. Slide 10613

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.308.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2. Slide 10611

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2. Slide 10196

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.301)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.301.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain replicate 2. Slide 10661

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to stationary phase (OD600 = 1.26)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 1.26.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain replicate 2 dye flip. Slide 10610

description: vs. reference

tag: Halobacterium sp. NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 1.26.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2 dye flip. Slide 10197

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2 dye flip. Slide 10193

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.227)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.227.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain replicate 2 dye flip . Slide 10195

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.792)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.792.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain replicate 2. Slide 10194

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.792.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 3. Slide 10615

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 2 dye flip. Slide 10189

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to early-log phase (OD600 = 0.133)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.133.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain replicate 2 dye flip . Slide 10191

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.553)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.553.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain replicate 2. Slide 10190

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.553.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain replicate 2 dye flip . Slide 10187

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to early-log phase (OD600 = 0.333)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.333.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain replicate 2. Slide 10186

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.333.

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm in complex medium (CM).


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2. Slide 10188

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain replicate 2. Slide 10192

description: vs. reference


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain. Slide 10164

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.815)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.815.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain dye flip. Slide 10165

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.815.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion strain dye flip. Slide 10161

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.503)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in standard growth medium at 37C, cell density OD600 = 0.503.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain. Slide 10162

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to mid-log phase (OD600 = 0.371)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.371.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain dye flip. Slide 10167

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to late-log phase (OD600 = 0.419)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.419.


title: Halobacterium sp. NRC-1 growth curve  in VNG1451C deletion strain replicate 3 dye flip. Slide 10684

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to stationary phase (OD600 = 0.56)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.56.


title: Halobacterium sp. NRC-1 growth curve in ura3 deletion parent strain. Slide 10160

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in standard growth medium at 37C, cell density OD600 = 0.503.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain. Slide 10166

description: vs. reference

tag: Halobacterium sp. NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: ura3 deletion strain replicate 2 dye flip Slide 11561 stationary phase (OD600 = 0.53) defined media with 10% glucose

description: vs. reference

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286. The analysis pipeline sets the ratio to 1 for any spots where the intensity is below 2 times the standard deviation of the background in both channels. This essentially acts as a filter for subsequent steps. The normalization is done on the 75th percentile of intensities of the two channels.

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.53)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.53.


title: VNG1451C deletion strain replicate 2 Slide 11564 stationary phase (OD600 = 0.76) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.76)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.76.


title: ura3 deletion parent strain replicate 2 Slide 11562 stationary phase (OD600 = 1.60) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) without glucose to stationary phase (OD600 = 1.60)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 1.60.


title: VNG1451C deletion strain replicate 2 dye flip Slide 11567 mid-log phase (OD600 = 0.355) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.355)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without 10% glucose at 37C, cell density OD600 = 0.355.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain dye flip. Slide 10163

description: vs. reference


title: Halobacterium sp. NRC-1 defined media glucose growth curve in ura3 deletion strain replicate 2 dye flip. Slide 11563

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to stationary phase (OD600 = 1.60)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 1.60.


title: VNG1451C deletion strain replicate 2 dye flip Slide 11557 mid-log phase (OD600 = 0.302) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.302)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.302.


title: VNG1451C deletion strain replicate 2 Slide 11556 mid-log phase (OD600 = 0.302) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.302)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain dye flip. Slide 10159

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in rich media (CM) to early-log phase (OD600 = 0.190(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in standard growth medium at 37C, cell density OD600 = 0.190.


title: VNG1451C deletion strain replicate 2 Slide 11566 stationary phase (OD600 = 0.355) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to stationary phase (OD600 = 0.355)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.355.


title: VNG1451C deletion strain replicate 2 dye flip Slide 11565 stationary phase (OD600 = 0.76) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.76)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.


title: Halobacterium sp. NRC-1 growth curve in VNG1451C deletion strain. Slide 10158

description: vs. reference


title: ura3 deletion strain replicate 2 dye flip Slide 11555 mid-log phase (OD600 = 0.701) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to mid-log phase (OD600 = 0.701)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 0.701.


title: VNG1451C deletion strain replicate 2 dye flip Slide 11559 mid-log phase (OD600 = 0.108) defined media without glucose

description: vs. reference

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm in complex medium (CM).

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.108)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without 10% glucose at 37C, cell density OD600 = 0.108.


title: VNG1451C deletion strain replicate 2 Slide 11558 mid-log phase (OD600 = 0.108) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.108)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.108.


title: ura3 deletion parent strain replicate 2 Slide 11560 stationary phase (OD600 = 0.53) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.53.


title: VNG1451C deletion strain replicate 2 dye flip Slide 11549 early-log phase (OD600 = 0.230) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.230)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.230.


title: ura3 deletion parent strain replicate 2 Slide 11546 early-log phase (OD600 = 0.214) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to early-log phase (OD600 = 0.214)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.214.


title: ura3 deletion strain replicate 2 dye flip Slide 11545 early-log phase (OD600 = 0.182) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.182)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.182.


title: VNG1451C deletion strain replicate 2 Slide 11548 early-log phase (OD600 = 0.230) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.230)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.


title: ura3 deletion strain replicate 2 dye flip Slide 11553 mid-log phase (OD600 = 0.291) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.291)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.291.


title: VNG1451C deletion strain Slide 11469 mid-log phase (OD600 = 0.314) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.314)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.314.

tag: Halobacterium sp. NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: ura3 deletion strain replicate 2 dye flip Slide 11547 early-log phase (OD600 = 0.214) defined media without glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 0.214.


title: VNG1451C deletion strain Slide 11530 stationary phase (OD600 = 0.80) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.80)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.80.


title: ura3 deletion strain dye flip Slide 11476 stationary phase (OD600 = 1.47) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to stationary phase (OD600 = 1.47)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 1.47.


title: ura3 deletion parent strain Slide 11475 stationary phase (OD600 = 1.47) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) without glucose to stationary phase (OD600 = 1.47)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 1.47.


title: ura3 deletion parent strain replicate 2 Slide 11552 mid-log phase (OD600 = 0.291) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.291.


title: ura3 deletion strain dye flip Slide 11468 mid-log phase (OD600 = 0.641) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to mid-log phase (OD600 = 0.641)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 0.641.


title: ura3 deletion parent strain Slide 11465 mid-log phase (OD600 = 0.304) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.304)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.304.

source_name: Halobacterium sp. NRC-1


title: VNG1451C deletion strain Slide 11542 stationary phase (OD600 = 0.36) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to stationary phase (OD600 = 0.36)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.36.


title: VNG1451C deletion strain dye flip Slide 11531 stationary phase (OD600 = 0.80) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.80)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.


title: ura3 deletion strain dye flip Slide 11474 stationary phase (OD600 = 0.5) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to stationary phase (OD600 = 0.5)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.5.


title: ura3 deletion parent strain replicate 2 Slide 11554 mid-log phase (OD600 = 0.701) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to mid-log phase (OD600 = 0.701)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.701.

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm in complex medium (CM).


title: VNG1451C deletion strain dye flip Slide 11541 early-log phase (OD600 = 0.042) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to early-log phase (OD600 = 0.042)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without 10% glucose at 37C, cell density OD600 = 0.042.


title: VNG1451C deletion strain dye flip Slide 11472 mid-log phase (OD600 = 0.104) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.104)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without 10% glucose at 37C, cell density OD600 = 0.104.


title: ura3 deletion parent strain replicate 2 Slide 11544 early-log phase (OD600 = 0.182) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.182.


title: ura3 deletion parent strain Slide 11473 stationary phase (OD600 = 0.5) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.5.


title: ura3 deletion parent strain Slide 11467 mid-log phase (OD600 = 0.641) defined media without glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.641.


title: ura3 deletion strain dye flip Slide 11466 mid-log phase (OD600 = 0.304) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.304.


title: VNG1451C deletion strain dye flip Slide 11470 mid-log phase (OD600 = 0.314) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to mid-log phase (OD600 = 0.314)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.314.


title: VNG1451C deletion strain dye flip Slide 11543 mid-log phase (OD600 = 0.36) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.36)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without 10% glucose at 37C, cell density OD600 = 0.36.


title: VNG1451C deletion strain Slide 11540 early-log phase (OD600 = 0.042) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to early-log phase (OD600 = 0.042)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.042.


title: VNG1451C deletion strain Slide 11471 mid-log phase (OD600 = 0.104) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) without glucose to mid-log phase (OD600 = 0.104)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.104.


title: ura3 deletion strain dye flip Slide 11537 early-log phase (OD600 = 0.210) defined media without glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) to early-log phase (OD600 = 0.210)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium without glucose at 37C, cell density OD600 = 0.210.


title: ura3 deletion parent strain Slide 11536 early-log phase (OD600 = 0.210) defined media without glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium without glucose at 37C, cell density OD600 = 0.210.


title: ura3 deletion strain dye flip Slide 11535 early-log phase (OD600 = 0.192) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 ura3 deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.192)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 ura3 deletion parent in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.192.


title: VNG1451C deletion strain Slide 11538 early-log phase (OD600 = 0.222) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.222)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light at 37C.

tag: Halobacterium sp. NRC-1 VNG1451C deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.222.


title: ura3 deletion parent strain Slide 11534 early-log phase (OD600 = 0.192) defined media with 10% glucose

description: vs. reference

tag: Halobacterium sp. NRC-1 ura3 deletion in defined growth medium with 10% glucose at 37C, cell density OD600 = 0.192.


title: HOB IN1

type: genomic

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

description: Input DNA - Replicate 1

hyb_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)

data_processing: The Me-DIP-chip .cel files for HOB, U2OS and MG63 (2 IP and 2 IN) were log2 transformed, normalized and imported into Partek Genomic Suite Software as previously described [ Sadikovic B, Andrews J, Carter D, Robinson J, Rodenhiser DI (2008) Genome-wide H3K9 histone acetylation profiles are altered in benzopyrene-treated MCF7 breast cancer cells. J Biol Chem 283: 4051-4060]. We baseline normalized the signal using the matched-pair normalization tool in PGS, by subtracting log2 IN signal intensity at each of 4.2 million from cell type-matched IP signals resulting in 6  corrected datasets (IP1 cor. and IP2 cor. for each cell line). In order to determine the relative enrichment of IP cor. signals in U2OS or MG63 relative to  HOB, we used the PGS 1-way ANOVA tool and calculated the fold change using the geometric mean (for log-transformed data).  Thus generated signals represented baseline-normalized, HOB-relative, and cancer cell-specific enrichment levels for each of 4.2 million probes. Significant region detection (both enrichment/hypermethylation and depletion/hypomethylation) was performed using Hidden Markov Model (HMM) tool in PGA by applying it to the fold change data for both U2OS and MG63. In order to capture significant differences in enrichment in each cancer cell line vs. HOB across shorter genomic regions (min. ~350 nucleotides) with robust enrichment differences as well as intermediate (min. ~500 nucleotides) and large regions (min. 1400 nucleotides), three HMM algorithms were applied (s-HMM, m-HMM, and l-HMM). Following cutoffs were used: s-HMM (min. probes: 10, detection states: -5,5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 2), m-HMM (min. probes: 15, detection states: -3,3, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1), and l-HMM  (min. probes: 40, detection states: -1.5,1.5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1). Significantly enriched/hypermethylated and depleted/hypomethylated HMM regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the  HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Normalized data provided as Series supplementary file.

label: streptavidin/phycoerythrin

molecule: genomic DNA

source_name: normal osteoblasts

growth_protocol: The human OS cell lines U2OS (ATCC # HTB-96) and MG63 (ATCC # CRL-1427) were purchased from American Type Culture Collection ATCC (Rockville, MD) and maintained in alpha-Minimum Essential Medium (alpha-MEM) supplemented with 10% heat inactivated Fetal Bovine Serum and 2 mM L-Glutamine. Normal human osteoblasts (HOB) are primary osteoblasts from the hip bone of a normal male donor that were purchased from PromoCell (Heidelberg, Germany, Catalogue # C-12760) and maintained in medium provided by the manufacturer and used at culture passage 3. Three days after plating (~80% confluent), cells where harvested for DNA or RNA extractions.

extract_protocol: DNA was extracted by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water

treatment_protocol: Cells were harvested with Trypsin (Invitrogen) as per manifacturer's instructions

tag: Normal Human Osteoblast Cells from healthy male donor (Heidelberg, Germany, Catalogue # C-12760)


title: HOB IP1

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 1

scan_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: HOB IP2

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 2

label_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: HOB IN2

description: Input DNA - Replicate 2


title: VNG1451C deletion strain dye flip Slide 11539 early-log phase (OD600 = 0.222) defined media with 10% glucose

description: vs. reference

growth_protocol: Halobacterium sp. NRC-1 VNG1451C deletion strain was grown in defined media (CDM) supplemented with 10% glucose to early-log phase (OD600 = 0.222)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with glycerol dye flip. Slide 11697

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 0.965 in standard growth media with 20microgram/ml mevinolin and glycerol versus an IP from the same sample.

source_name: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain WCE fraction.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 1mL/L glycerol and 20 ug/mL mevinolin to stationary phase (OD600 = 0.965)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

extract_protocol: Cells were cross-linked with 1.2% formaldehyde and subsequently lysed via sonication. DNA was sheared via sonication. A small fraction of total DNA was kept for a whole cell extract (wce) background while the rest of the DNA was immunoprecipitated with antibody against the epitope tag in question. Each DNA sample was treated with protease and RNAase and amplified by PCR utilizing ligated universal linkers as templates for amplification. The resulting DNA was cleaned and quantified.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) with glycerol at 37C, cell density OD600 = 0.965.

source_name: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP faction.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with glycerol and 20 ug/mL mevinolin to stationary phase (OD600 = 0.965)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with glycerol at 37C, cell density OD600 = 0.965.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with glycerol. Slide 11696

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 0.965 in standard growth media with 20microgram/ml mevinolin and glycerol versus a whole cell extract from the same sample.

source_name: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin and 1mL/L glycerol to stationary phase (OD600 = 0.965)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

source_name: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with high glucose replicate 2. Slide 11692

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 3.829 in standard growth media with 20microgram/ml mevinolin and high glucose versus a whole cell extract from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin and 10% glucose to stationary phase (OD600 = 3.829)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with high gluose at 37C, cell density OD600 = 3.829.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) with high glucose at 37C, cell density OD600 = 3.829.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with high glucose replicate 1. Slide 11684


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with high glucose replicate 2 dye flip. Slide 11693

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 3.829 in standard growth media with 20microgram/ml mevinolin and high glucose versus an IP from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 10% glucose and 20 ug/mL mevinolin to stationary phase (OD600 = 3.829)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with high glucose at 37C, cell density OD600 = 3.829.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with high glucose replicate 1 dye flip. Slide 11685


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose, high cell density repl 2. Slide 11698

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.607 in standard growth media with 20microgram/ml mevinolin and low glucose versus a whole cell extract from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin and 0.1% glucose to stationary phase (OD600 = 1.607)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with low gluose at 37C, cell density OD600 = 1.607.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) with low glucose at 37C, cell density OD600 = 1.607.


title: shep090|K-D-138

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48959.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

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), default computed normalization procedure, see SMD website

source_name: Human female genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Human female genomic DNA

source_name: Breast tumor genomic DNA

tag: Breast tumor genomic DNA


title: shep023|K-D-009

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46365.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose high cell density repl 2 dye flip. Slide 11699

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.607 in standard growth media with 20microgram/ml mevinolin and low glucose versus an IP from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 0.1% glucose and 20 ug/mL mevinolin to stationary phase (OD600 = 1.607)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with low glucose at 37C, cell density OD600 = 1.607.


title: shep235|K-D-129

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49125.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose high cell density repl 1 dye flip. Slide 11687


title: shep112|K-D-117

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48961.gif


title: shep065|K-D-003

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48413.gif


title: shep113|K-D-128

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48962.gif


title: shep162|K-D-143

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48971.gif


title: shep044|K-D-005

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48408.gif


title: shep137|K-D-127

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48966.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose replicate 2 dye flip. Slide 11189

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 0.579 in standard growth media with 20microgram/ml mevinolin and low glucose versus an IP from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 0.1% glucose and 20 ug/mL mevinolin to mid-log phase (OD600 = 0.579)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) with low glucose at 37C, cell density OD600 = 0.579.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with low glucose at 37C, cell density OD600 = 0.579.


title: shep022|K-D-080

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/46278.gif

source_name: Human breast tumor genomic DNA

tag: Human breast tumor genomic DNA


title: shep061|K-D-050

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48409.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose, high cell density repl 1. Slide 11686


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose replicate 2. Slide 11188

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 0.579 in standard growth media with 20microgram/ml mevinolin and low glucose versus a whole cell extract from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin and 0.1% glucose to mid-log phase (OD600 = 0.579)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) with low gluose at 37C, cell density OD600 = 0.579.


title: shep042|K-D-047

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48406.gif


title: shep088|K-D-016

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48956.gif


title: shep021|K-D-021

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46347.gif


title: shep140|K-D-115

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48969.gif


title: shep040|K-D-034

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46367.gif


title: shep232|K-D-061

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49121.gif


title: shep164|K-D-125

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48973.gif


title: shep111|K-D-116

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48960.gif


title: ULLG_T-069

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51261.gif


title: shep089|K-D-031

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48957.gif


title: shep087|K-D-030

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48955.gif


title: ULL_T-101

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51574.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose replicate 1. Slide 11458


title: shep024|K-D-120

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46366.gif


title: ULLG_T-199

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51265.gif


title: shep233|K-D-020

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49122.gif


title: ULL_T-183

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51572.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 6 dye flip. Slide 11695

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.049 in standard growth media with 20microgram/ml mevinolin versus an IP from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to stationary phase (OD600 = 1.049)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) at 37C, cell density OD600 = 1.049.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) at 37C, cell density OD600 = 1.049.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 5 dye flip. Slide 11691


title: ULL_T-167II

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51576.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 5. Slide 11690

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.049 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample.


title: shep063|K-D-015

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48411.gif


title: ULLG_T-113II

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51258.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 6. Slide 11694


title: shep043|K-D-017

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48407.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 4 dye flip. Slide 11689


title: ULL_T-165

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51579.gif


title: ULL_T-036

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51568.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 4. Slide 11688


title: shep236|K-D-022

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49126.gif


title: shep163|K-D-142

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48972.gif


title: ULL_T-132

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51569.gif


title: shep064|K-D-112

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48412.gif


title: ULLG_T-085

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51267.gif


title: shep136|K-D-137

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48965.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip with low glucose replicate 1 dye flip. Slide 11459

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 0.579 in standard growth media with 20microgram/ml mevinolin and low glucose versus an IP from the same sample.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 3. Slide 11398

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.03 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to stationary phase (OD600 = 1.03)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) at 37C, cell density OD600 = 1.03.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) at 37C, cell density OD600 = 1.03.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 3 dye flip. Slide 11399

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.03 in standard growth media with 20microgram/ml mevinolin versus an IP from the same sample.


title: ULLG_T-237

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51266.gif


title: ULL_T-112

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51570.gif


title: ULLG_T-123

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51260.gif


title: ULL_T-188

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51580.gif


title: ULLG_T-139

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51256.gif


title: ULL_T-144

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51573.gif


title: ULLG_T-062

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51263.gif


title: shep138|K-D-145

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48967.gif


title: shep161|K-D-130

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48970.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 2. Slide 11392

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.50 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to stationary phase (OD600 = 1.50)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) at 37C, cell density OD600 = 1.50.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) at 37C, cell density OD600 = 1.50.


title: ULL_T-096

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51578.gif


title: shep165|K-D-126

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48974.gif


title: ULLG_T-143

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51262.gif


title: ULLG_T-019

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51264.gif


title: ULLG_T-105

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51259.gif


title: norway 92_BC703B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51808.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 2 dye flip. Slide 11393

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.50 in standard growth media with 20microgram/ml mevinolin versus an IP from the same sample.


title: liver WT #4 / liver from vitamin C treated Wrn mutant #4

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: WT #4 vs. vitamin C treated Wrn mutant #4

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing: Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method.

source_name: liver from wild type animal

label_protocol: Protocol from Agilent

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

tag: Strain

source_name: liver from vitamin C treated Wrn mutant


title: ULL_T-053

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51577.gif


title: shep086|K-D-124

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48414.gif


title: norway 4_BC104A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51762.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 1b dye flip. Slide 11389

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.57 in standard growth media with 20microgram/ml mevinolin versus an IP from the same sample.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to stationary phase (OD600 = 1.57)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) at 37C, cell density OD600 = 1.57.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) at 37C, cell density OD600 = 1.54.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 1b. Slide 11388

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.57 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain IP fraction in standard growth medium (CM) at 37C, cell density OD600 = 1.68.

growth_protocol: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to stationary phase (OD600 = 1.68)(50mL culture in 125mL flask) in high oxgen (shaking at 225 RPM) and in light.


title: shep041|K-D-144

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48405.gif

tag: Human female genomic DNA


title: norway 6_BC106B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51767.gif

tag: Breast tumor genomic DNA


title: liver WT #3 / liver from vitamin C treated Wrn mutant #3

description: WT #3 vs. vitamin C treated Wrn mutant #3


title: norway 56_BC308B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51852.gif


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 1a dye flip. Slide 11387

description: WCE sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.68 in standard growth media with 20microgram/ml mevinolin versus an IP from the same sample.

tag: Halobacterium salinarum NRC-1 VNG1451C cmyc-tagged strain whole cell extract (WCE) faction in standard growth medium (CM) at 37C, cell density OD600 = 1.68.


title: Halobacterium salinarum NRC-1 VNG1451C ChIP-chip replicate 1a. Slide 11386

description: IP sample of Cmyc tagged VNG1451C expressed in Halobacterium NRC-1 cells grown to OD600 1.68 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample.


title: shep234|K-D-069

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49124.gif


title: shep062|K-D-132

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48410.gif


title: norway 64_BC405A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51801.gif


title: norway 85_BC610A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51806.gif


title: liver from vitamin C treated Wrn mutant #1 / liver WT #1

description: WT #1 vs. vitamin C treated Wrn mutant #1


title: liver from vitamin C treated Wrn mutant #2 / liver WT #2

description: WT #2 vs. vitamin C treated Wrn mutant #2


title: liver WT #4 / liver Wrn mutant #4

description: WT #4 vs. Wrn mutant #4

source_name: liver from Wrn mutant


title: norway 63_BC404B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51800.gif


title: shep115|K-D-114Q

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48963.gif


title: norway 80_BC605B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51804.gif


title: norway 5_BC105A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51765.gif


title: liver Wrn mutant #2 / liver WT #2

description: WT #2 vs. Wrn mutant #2


title: liver WT #3 / liver Wrn mutant #3

description: WT #3 vs. Wrn mutant #3


title: norway 15_BC115B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51776.gif


title: norway 18_BC118B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51823.gif


title: liver Wrn mutant #1 / liver WT #1

description: WT #1 vs. Wrn mutant #1


title: norway 16_BC116A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51817.gif


title: norway 102_BC710A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51863.gif


title: norway 101_BC709B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51811.gif


title: norway 41_BC208A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51850.gif


title: norway 55_BC307B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51798.gif


title: norway 22_BC120A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51780.gif


title: norway 111_BC807A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs//51813.gif


title: norway 11_BC111A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51815.gif


title: norway 47_BC213B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51796.gif


title: norway 37_BC205A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51791.gif


title: norway 83_BC608B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51805.gif


title: norway 112_BC808A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51867.gif


title: norway 43_BC210B-AF

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51868.gif


title: norway 12_BC112B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51773.gif


title: norway 29_BC125A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51788.gif


title: norway FU44_FU 44-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38971.gif

source_name: Normal female genomic DNA

tag: Normal female genomic DNA

source_name: FUMI44 genomic DNA

tag: FUMI44 genomic DNA


title: norway 65_BC406A-2ndTUMOR

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51802.gif


title: ULLG_T-002

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34825.gif

source_name: NB

tag: NB


title: norway 100_BC708B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51859.gif


title: norway 61_BC402B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51854.gif


title: norway 39_BC206A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51793.gif


title: ULLG_T-46

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41177.gif


title: norway 2_BC102B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51760.gif


title: norway 104_BC711B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51865.gif


title: norway 51_BC303B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51797.gif


title: norway 81_BC606B-AF

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51869.gif


title: norway 32_BC201B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51790.gif


title: norway 109_BC805A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51866.gif


title: norway 27_BC124A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51827.gif


title: norway 90_BC702B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51807.gif


title: norway FU12_FU 12-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38950.gif

source_name: FUMI12 genomic DNA

tag: FUMI12 genomic DNA


title: ULLG_T-031

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41211.gif


title: norway 21_BC119A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51778.gif


title: norway 95_BC713A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51812.gif


title: Agilent synthetic miRNA sample B #1

type: other

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: hybridization of synthetic RNA corresponding to human miRNA

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent DNA microarray scanner

data_processing: Feature extraction image analysis

molecule: other

source_name: Sample B

label_protocol: Agilent standard protocol

tag: sample

value: synthetic miRNA


title: norway FU37_FU 37-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38967.gif

source_name: FUMI37 genomic DNA

tag: FUMI37 genomic DNA


title: Agilent synthetic miRNA sample B #2


title: Agilent synthetic miRNA sample A #2

source_name: Sample A


title: norway 19_BC111B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51771.gif


title: total small RNAs from P. pacificus

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: adapter sequences (ctCCGAgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the P. pacificus genome (WUSTL assembly version 5.0.1).

label: not applicable

organism: Pristionchus pacificus

source_name: mixed stage animals

label_protocol: not applicable

extract_protocol: Total RNA extracted using miRVana miRNA isolation kit (Ambion). Small RNA fraction was isolated using PAGE. The RNAs were poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the small RNAs. First-strand cDNA synthesis was performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. The cDNA was PCR amplified and the 125 - 140 bp fraction of the cDNA pool was obtained by fractionation of the cDNA on a preparative 6% polyacrylamide gel. The eluted cDNA was purified using the Macherey & Nagel NucleoSpin Extract II kit and sequenced on 454 GS FLX system.

tag: strain

tag: developmental stage

value: mixed stages


title: norway 17_BC117A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51819.gif


title: Exiqon synthetic miRNA sample B #2

hyb_protocol: Exiqon standard protocol for miRNAs

label_protocol: Exiqon standard end labelling protocol for miRNAs


title: Exiqon synthetic miRNA sample B #1


title: ULLG_T-060

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35893.gif


title: ULLG_T-037

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39882.gif


title: norway FU23_FU 23-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38959.gif

source_name: FUMI23 genomic DNA

tag: FUMI23 genomic DNA


title: norway 53_BC305A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51851.gif


title: norway 48_BC214B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51794.gif


title: Agilent synthetic miRNA sample A #1


title: norway 7_BC107B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51769.gif


title: Exiqon synthetic miRNA sample A #1


title: ULLG_T-177

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37006.gif


title: norway 10_BC110B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51814.gif


title: norway FU45_FU 45-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38972.gif

source_name: FUMI45 genomic DNA

tag: FUMI45 genomic DNA


title: ULLG_T-075

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41403.gif

source_name: nb

tag: nb


title: norway 14_BC114A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51816.gif

source_name: Human female genomic DNA


title: norway 57_BC309A-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51799.gif

source_name: Breast tumor genomic DNA


title: ULLG_T-048II

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41210.gif


title: ULLG_T-023

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41052.gif