title: Human Ntera2 cells, E2F1 Replicate B

description: Human Ntera2 cells


title: Human HeLaS3 cells, E2F6 Replicate C

status: Public on Aug 22 2007

type: genomic

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

country: USA

institute: OSU Medical Center

description: Human HeLaS3 cells

hyb_protocol: Cy-labedled ChIP Samples

scan_protocol: NimbleScan

data_processing: log base 2 ratios

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLaS3 cells

label_protocol: Cy5 dye

extract_protocol: ChIP-chip

tag: E2F6 antibody

label_protocol: Cy3 dye

tag: control total input


title: Human Ntera2 cells, IGG Replicate A

description: Human Ntera2 cells

source_name: Ntera2 cells

tag: IGG antibody


title: Human Ntera2 cells, E2F1 Replicate A

description: Human Ntera2 cells

tag: E2F1 antibody


title: Human MCF7 cells, E2F4 Replicate B

description: Human MCF7 cells

source_name: MCF7 cells

tag: E2F4 antibody


title: Human HeLaS3 cells, E2F1 Replicate A

description: Human HeLaS3 cells


title: Human HeLaS3 cells, E2F4 Replicate B

description: Human HeLaS3 cells


title: Human HeLaS3 cells, E2F1 Replicate C

description: Human HeLaS3 cells


title: Human GM06990 cells, E2F6 Replicate C

description: Human GM06990 cells

source_name: GM06990 cells


title: Human HeLaS3 cells, E2F6 Replicate B

description: Human HeLaS3 cells


title: Human Ntera2 cells, E2F6 Replicate A

description: Human Ntera2 cells


title: Human GM06990 cells, E2F6 Replicate B

description: Human GM06990 cells


title: Human GM06990 cells, E2F1 Replicate B

description: Human GM06990 cells


title: Human Ntera2 cells, E2F4 Replicate C

description: Human Ntera2 cells


title: Human HeLaS3 cells, E2F6 Replicate A

description: Human HeLaS3 cells


title: Human Ntera2 cells, E2F6 Replicate B

description: Human Ntera2 cells


title: Human Ntera2 cells, E2F1 Replicate C

description: Human Ntera2 cells


title: Human GM06990 cells, E2F4 Replicate B

description: Human GM06990 cells


title: Human GM06990 cells, E2F4 Replicate C

description: Human GM06990 cells


title: Human MCF7 cells, E2F6 Replicate A

description: Human MCF7 cells


title: Human MCF10A cells, E2F6 Replicate A

description: Human MCF10A cells

source_name: MCF10A cells


title: Human Ntera2 cells, E2F4 Replicate A

description: Human Ntera2 cells


title: Human GM06990 cells, E2F4 Replicate A

description: Human GM06990 cells


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant. Rep 3

status: Public on Aug 21 2007

type: RNA

city: Stanford

first: SMD

last: Staff

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Biological replicate 4 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment

hyb_protocol: A 70-mer oligonucleotide-based microarray (tuberculosis oligonucleotide set; Qiagen) was used. Hybridization solution (10 ul; labelled cDNA, 5 ug of tRNA, 2x SSC, 25% formamide, 0.1% SDS) was hybridized at 52 C.

scan_protocol: Microarrays were scanned using a GenePix 4000 A (Axon Instruments). The intensities of the two dyes at each spot were quantified using SCANALYZE (M. Eisen; http://rana.lbl.gov/EisenSoftware.htm).

data_processing: Microarray-determined ratios were calculated from three biological replicates with two microarrays for each biological replicate. The overall reproducibility of the microarray experiments was evaluated using the Signifi-cance Analysis of Microarrays (SAM) program.  The SAM algorithm was set for two-class unpaired analysis with 500 permutations and K-nearest imputer for missing data. Significantly regulated genes were selected by adjusting the delta value to give a false discovery rate below 1%. In each data set, all genes regulated 1.5-fold and greater were determined to be significant with a false discovery rate of less than 1%, indicating a high degree of reproducibility.

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Cell culture grew under any treatment

label_protocol: Labelled cDNA was prepared as follows: 2 ug of total RNA and 4.4 ug of random oligonucleotide hexamers were incubated for 2 min at 98 C, cooled on ice, combined with Stratascript RTase buffer, 0.5 mM dA-, G-, CTP, 0.02 mM dTTP, 1.5 nmol of Cy3- or Cy5-dUTP (Amersham) and 1.8 ul of Stratascript RTase (Stratagene) in a total volume of 25 ul and incubated for 10 min at 25 C and for 90 min at 42 C. cDNA was purified by microcon-10 (Amicon) filtration.

growth_protocol: H37Rv (ATCC 27294), H37RdeltadosR::kan and M. bovis BCG-Montreal (ATCC 35735) were grown to mid-log phase in 7H9 media with 0.05% Tween 80 and ADC supplement (Becton Dickinson) and stored as 1 ml aliquots in 15% glycerol (final concentration) at -80 C. For individual experiments, bacilli were grown in roller bottles in Middlebrook 7H9 medium (Becton Dickinson) with 0.05% Tween 80 and ADC supplement or on Middlebrook 7H10 plates at 37 C as described previously . When needed, kanamycin was used at 30 ug/ml (50 ug/ml for E. coli) and hygromycin at 50 ug/ml (200 ug/ml for E. coli).

extract_protocol: Cells were disrupted by three 30-sec pulses in a BioSpec Products bead beater. After 5 min at room temperature, samples were centrifuged at 13,000 x g for 45 sec, and the supernatants were extracted with 300 ul of chloroformyisoamyl alcohol (24:1) and precipitated with isopropyl alcohol. Samples were incubated 10 min to overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1 ml of 75% ethanol, centrifuged at 13,000 x g for 5 min, and air-dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x buffer and 4 units of DNase I (Ambion, Austin, TX) were added and the samples were incubated for 30 min. Final purification of RNA was by RNeasy column (Qiagen, Chatsworth, CA).

treatment_protocol: Frozen cell pellets were suspended in 1 ml of Trizol reagent (GIBCOy BRL) and transferred to 2-ml screw-cap tubes containing 0.4-ml of 0.1-mm diameter zirconiaysilica beads (BioSpec Products, Bartlesville, OK).

tag: Rv3133 (H37Rv Delta-DosR::Kan)

source_name: Cell culture grew under 0.2% Oxygen treatment


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant. Rep 2

description: Biological replicate 3 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment


title: Human MCF7 cells, E2F6 Replicate C

description: Human MCF7 cells


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant. Rep 4

description: Biological replicate 5 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant. Rep 5

description: Biological replicate 6 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment


title: Human MCF7 cells, E2F1 Replicate B

description: Human MCF7 cells


title: Human GM06990 cells, E2F1 Replicate C

description: Human GM06990 cells


title: Human Ntera2 cells, E2F6 Replicate C

description: Human Ntera2 cells


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant

description: Biological replicate 1 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment


title: Human GM06990 cells, E2F6 Replicate B

description: Human GM06990 cells


title: Hypoxic conditions experiment of M. tuberculosis wild type. Rep 3

description: Biological replicate 4 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment

tag: H37Rv (ATCC 27294 wild_type)


title: Hypoxic conditions experiment of M. tuberculosis wild type. Rep 4

description: Biological replicate 5 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment


title: Hypoxic conditions experiment of M. tuberculosis wild type. Rep 2

description: Biological replicate 3 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment


title: Human Ntera2 cells, E2F6 Replicate A

description: Human Ntera2 cells


title: Human MCF10A cells, E2F6 Replicate B

description: Human MCF10A cells


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 12

description: Biological replicate 7 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.

hyb_protocol: DNA microarray experiments were performed using a whole genome microarray of M. tuberculosis H37Rv prepared in the laboratory of Dr P. Butcher (St. George's Hospital Medical School, London).  Hybridization of microarray slides was performed under a coverslip as described (Wilson et al., 1999) in hybridization chambers at 60 C for 16Ð24 h and washed in 1x SSC, 0.005% SDS for 2 min and in 0.06x SSC for 4 min.

scan_protocol: Microarray slides were scanned for fluorescence with an Axon 4000A microarray scanner, local background subtracted using the GenePix software and normalized equivalent readings were plotted using GeneSpring software (Silicon Genetics).

data_processing: Data were obtained from at least six slides, including dye swaps. To account for dye swap, the signal channel and control channel measurements for dye swap samples were reversed. Each gene's measured intensity (wild type) was divided by its control channel value (mutant) in each sample to give the ratio of expression; if the control channel were below 10 then 10 was used instead. If the control channel and the signal channel were both below 10 then no data was reported. The 50th percentile of all measurements was used as a positive control for each sample; each measurement for each gene was divided by this synthetic positive control. The percentile was calculated using only genes marked present. This normalizes each array so that the 50th percentile/median measurement (ratio) for each array is equal to 1 and ensures that any systematic effects are removed (caused by scanning, labelling, hybridization, etc.), enabling valid comparison between different arrays as each array is scaled/transformed to have the same median value. Genes were defined as being differentially regulated where there was a greater than twofold change in at least four of the hybridizations and where P < 0.05 by Student's t-test. The t-test was conducted on the six experiments as a group. To limit the list of genes it was arbitrarily limited to those with a 2.4-fold increase or decrease in expression.

source_name: Cell culture grew in roller bottles containing Dubos medium

label_protocol: Fluorescently labelled cDNA copies of total RNA (5Ð10 ug) were generated by direct incorporation of Cy3- or Cy5-labelled dCTP (Amersham) using 6 ug of random hexamers together with 500 units Superscript RNase H- reverse transcriptase (GibcoBRL), 1x first-strand buffer, 10 mM DTT, dNTPs (40 uM dCTP, 100 uM each of dATP, dGTP, dTTP) and 1.5 nmol Cy3 or Cy5 labelled dCTP. RNA and random primers were heated at 95 C for 5 min in a final volume of 11 ul, snap cooled before adding the remaining components. Incubation was at 25 C for 10 min, followed by 42 C for 90 min. The two labelled samples to be compared (Cy3 and Cy5) were combined and purified using MinElute columns (Qiagen) and the pellets resuspended in 12.5 ul of water, 4x SSC, 0.3% SDS, heated at 95 C for 2 min.

growth_protocol: Bacteria were grown in Dubos medium (supplemented with 0.2% v/v glycerol, 4% v/v Dubos medium albumin) in roller bottles at 37 C. Growth was measured at OD600 and bacteria were harvested at mid-exponential phase.

extract_protocol: Total RNA was extracted using a Hybaid RNA isolation kit (Hybaid). RNA was purified using RNeasy columns (Qiagen) between treatments. RNA was checked for DNA contamination by PCR.

treatment_protocol: RNA was treated twice with RNase-free DNase (Roche) in the presence of 1 unit ml-1 RNasin ribonuclease inhibitor (Promega), 20 mM sodium acetate, 10 mM magnesium chloride and 10 mM sodium chloride

tag: Rv3676 (H37Rv-DeltaRv3676::hyg)

tag: H37Rv (wild_type)


title: Human Ntera2 cells, E2F4 Replicate B

description: Human Ntera2 cells


title: Hypoxic conditions experiment of M. tuberculosis wild type

description: Biological replicate 1 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment


title: Human MCF10A cells, E2F4 Replicate B

description: Human MCF10A cells


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 11

description: Biological replicate 6 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Hypoxic conditions experiment of M. tuberculosis wild type. Rep 1

description: Biological replicate 2 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 13

description: Biological replicate 7 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Hypoxic conditions experiment of M. tuberculosis dosR mutant. Rep 1

description: Biological replicate 2 of 6. H37Rv dosR mutant grew under 0.2% Oxygen treatment


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 10

description: Biological replicate 6 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Human GM06990 cells, PolII Replicate C

description: Human GM06990 cells

tag: PolII antibody


title: Human MCF10A cells, E2F1 Replicate B

description: Human MCF10A cells


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 8

description: Biological replicate 5 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Human GM06990 cells, E2F6 Replicate A

description: Human GM06990 cells


title: Human MCF7 cells, E2F4 Replicate A

description: Human MCF7 cells


title: UlimD.3

city: Princeton

first: John

middle: Charles

last: Matese

state: NJ

address: Washington Rd.

department: Lewis-Sigler Institute

institute: Princeton University

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 11:44:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

source_name: Glucose limited D=0.25

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.25

extract_protocol: Extraction method : Qiagen Rneasy Kit

tag: Strain Name

source_name: Uracil limited D=0.329

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.329


title: Human MCF10A cells, E2F4 Replicate A

description: Human MCF10A cells


title: Human GM06990 cells, TAF1 Replicate C

description: Human GM06990 cells

tag: TAF1 antibody


title: Human GM06990 cells, TAF1 Replicate A

description: Human GM06990 cells


title: Human GM06990 cells, E2F4 Replicate B

description: Human GM06990 cells


title: Hypoxic conditions experiment of M. tuberculosis wild type. Rep 5

description: Biological replicate 6 of 6. H37Rv (wild type) grew under 0.2% Oxygen treatment


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 3

description: Biological replicate 2 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 2

description: Biological replicate 2 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Human GM06990 cells, PolII Replicate A

description: Human GM06990 cells


title: UlimD.25

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 11:37:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Uracil limited D=0.282

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.282


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 1

description: Biological replicate 1 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 7

description: Biological replicate 4 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 6

description: Biological replicate 4 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 9

description: Biological replicate 5 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Human MCF10A cells, E2F1 Replicate A

description: Human MCF10A cells


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 4

description: Biological replicate 3 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant

description: Biological replicate 1 of 7. Comparison between M. tuberculosis CPR like mutant and wild type. Cell culture grew in Dubos medium.


title: Comparison between M. tuberculosis wild type and M. tuberculosis CPR like mutant. Rep 5

description: Biological replicate 3 of 7. Comparison between M. tuberculosis wild type and CPR like mutant. Cell culture grew in Dubos medium.


title: Human GM06990 cells, PolII Replicate B

description: Human GM06990 cells


title: UlimD.2

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:16:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Uracil limited D=0.221

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.221


title: LlimD.25

source_name: Leucine limited D=0.282

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.282


title: UlimD.1

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-04 Scan Time : 11:41:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Uracil limited D=0.105

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.105


title: LlimD.3

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-01 Scan Time : 12:24:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Leucine limited D=0.336

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.336


title: UlimD.05

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-04 Scan Time : 11:33:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Uracil limited D=0.051

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.051


title: UlimD.15

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 11:28:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Uracil limited D=0.144

growth_protocol:
limiting nutrient : uracil
dilution rate : D=0.144


title: Head kidney,vaccine FO-8, pool 1C-rep6

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

description: Head kidney,vaccine FO-8, pool 1C-rep6

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hours. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

scan_protocol: Imaging was done at 10 µm resolution using ScanArray™ Express microarray scanner (Packard Bioscience). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively, at the same laser power (90%), with adjusted photomultiplier tube settings between slides to balance the Cy5 and Cy3 channels. Image analysis and fluorescent intensity data was extracted from Tiff images using ImaGene™ 5.6 Standard Edition softwareScanning was done using ScanArray™ Express microarray skanner

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Genespring GX software was used.

organism: Salmo salar

source_name: Total RNA from head kidney at 12 weeks post vaccination

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3 µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30 min in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30 µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.

growth_protocol: Atlantic salmon (Salmo salar) parr were reared in two 500 L tanks containing continuously running fresh water at an average temperature of 17 °C. Fish were fed with commercial dry pellets (EWOS, Norway).

extract_protocol: Total RNA extracted using RNEasy® kit with on column DNAse treatment

treatment_protocol: Fish were divided into 4 groups of 50 each by dip netting and sequencial allocation. Two groups (100 fish) were kept in each tank. Marking was done by finn clipping under anaesthesia (0.5 ml/L Chlorobutanol (Sigma)). Each fish was intraperitoneally injected with 0.1 ml of experimental water-in-oil vaccines (Pharmaq, Norway).

tag: Bolax strain

tag: Fish vaccinated with M.viscosa (6x standard antigen concentration)

tag: average side effect score

tag: average injection site inflammatory score=3.82

tag: average weight(g)=98.1

treatment_protocol: Fish were divided into 4 groups of 50 each by dip netting and sequencial allocation. Two groups (100 fish) were kept in each tank. Marking was done by fin clipping under anaesthesia (0.5 ml/L Chlorobutanol (Sigma)). Each fish was intraperitoneally injected with 0.1 ml of experimental water-in-oil vaccines (Pharmaq, Norway).

tag: Fish vaccinated with A. salmonicida (standard antigen concentration)

tag: average side effect score= 0.15

tag: average injection site inflammatory score=0.05

tag: average weight(g)=109.7


title: LlimD.15

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 11:52:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Leucine limited D=0.168

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.168


title: Head kidney,vaccine FO-8, pool 1C-rep5

description: Head kidney,vaccine FO-8, pool 1C-rep5

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average side effect score:3.00

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3 µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5µl of coupling buffer. Thereafter, 5.5µl of dye was added to the aRNA:coupling buffer and incubated for 30minutes in the dark. 2.25µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75µl of water to obtain a total volume to 30µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.


title: LlimD.05

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:00:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Leucine limited D=0.055

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.055


title: Head kidney,vaccine FO-7, pool 3C-rep6

description: Head kidney,vaccine FO-7 pool 3C-rep6

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16hrs. The arrays were washed first in (2X SSC, 0.1%SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: Fish vaccinated with M.viscosa (standard antigen concentration)

tag: average injection site inflammatory score=0.49

tag: average weight(g)=103.0

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3 µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30minutes in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30 µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.

tag: average side effect score=0.15


title: SlimD.15

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:08:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Sulfate limited D=0.166

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.166


title: Head kidney,vaccine FO-7, pool 3C-rep5

description: Head kidney,vaccine FO-7, pool 3C-rep5

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average side effect score:2.06

growth_protocol: Atlantic salmon (Salmo salar) parr were reared in two 500L tanks containing continuously running fresh water at an average temperature of 17 °C. Fish were fed with commercial dry pellets (EWOS, Norway).


title: SlimD.05

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-14 Scan Time : 10:49:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

tag: Strain Name

source_name: Sulfate limited D=0.054

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.054


title: SlimD.1

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-01 Scan Time : 12:16:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Sulfate limited D=0.1

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.1


title: Head kidney,vaccine FO-8, pool 1A-rep1

description: Head kidney,vaccine FO-8, pool 1A-rep1

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average side effect score= 0.15 average injection site inflammatory score=0.05


title: Head kidney,vaccine FO-8, pool 1B-rep4

description: Head kidney,vaccine FO-8, pool 1B-rep4

tag: Bolax strain


title: SlimD.2

source_name: Sulfate limited D=0.214

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.214


title: LlimD.2

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.25

source_name: Leucine limited D=0.21

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.21


title: SlimD.25

source_name: Glucose limited D=0.25

source_name: Sulfate limited D=0.276

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.276


title: Head kidney,vaccine FO-8, pool 1A-rep2

description: Head kidney,vaccine FO-8, pool 1A-rep2

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5min in 1X SSC, 4 X 5min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: Fish vaccinated with M.viscosa (6x standard antigen concentration)

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3 µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30 min in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.


title: LlimD.1

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-01 Scan Time : 12:00:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Leucine limited D=0.102

growth_protocol:
limiting nutrient : leucine
dilution rate : D=0.102


title: SlimD.3

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-01 Scan Time : 12:08:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Sulfate limited D=0.3

growth_protocol:
limiting nutrient : sulfate
dilution rate : D=0.3


title: Head kidney,vaccine FO-8, pool 1B-rep3

description: Head kidney,vaccine FO-8, pool 1B-rep3

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100°C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1%SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3 µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30 minutes in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30 µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30minutes in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30 µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.


title: Head kidney,vaccine FO-7, pool 3B-rep4

description: Head kidney,vaccine FO-7, pool 3B-rep4

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average side effect score


title: PlimD.25 2

description: PlimD.25 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-30 Scan Time : 15:39:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Phosphate limited D=.25

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.25


title: Head kidney,vaccine FO-7, pool 3A-rep1

description: Head kidney,vaccine FO-7, pool 3A-rep1

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hours. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average side effect score:2.04


title: PlimD.3 2

description: PlimD.3 2

source_name: Phosphate limited D=.3

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.3


title: Head kidney,vaccine FO-7, pool 3A-rep2

description: Head kidney,vaccine FO-7, pool 3A-rep2

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5 min in (2X SSC, 0.1%SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.


title: Head kidney,vaccine FO-7, pool 3B-rep3

description: Head kidney,vaccine FO-7, pool 3B-rep3

tag: average side effect score:2.05


title: PlimD.15 2

description: PlimD.15 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-30 Scan Time : 15:55:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Phosphate limited D=.15

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.15


title: PlimD.2 2

description: PlimD.2 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-30 Scan Time : 15:47:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Phosphate limited D=.2

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.2


title: Human GM06990 cells, TAF1 Replicate B

description: Human GM06990 cells

scan_protocol: NimbleScan

source_name: GM06990 cells

tag: TAF1 antibody

tag: control total input


title: NlimD.25

source_name: Nitrate limited D=0.279

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.279


title: NlimD.3

source_name: Nitrate limited D=0.3

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.3


title: Head kidney,vaccine FO-2, pool 2B-rep4

description: Head kidney,vaccine FO-2, pool 2B-rep4

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49  °C in a water bath for 1½ hours. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C , 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

source_name: Total RNA from head kidney at 12 weeks post vaccination

growth_protocol: Atlantic salmon (Salmo salar) parr were reared in two 500 L tanks containing continuously running fresh water at an average temperature of 17 °C. Fish were fed with commercial dry pellets (EWOS, Norway).

tag: Fish vaccinated with A. salmonicida (6x standard antigen concentration)

tag: average injection site inflammatory score=0.59

tag: average weight(g)=114.12

tag: Fish vaccinated with A. salmonicida (standard antigen concentration)

tag: average side effect score= 0.15

tag: average injection site inflammatory score=0.05


title: PlimD.1 2

description: PlimD.1 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-30 Scan Time : 15:31:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Phosphate limited D=.1

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.1


title: Head kidney,vaccine FO-2, pool 2C-rep5

description: Head kidney,vaccine FO-2, pool 2C-rep5

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hours. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49° C, 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

tag: average weight(g)=114.13

tag: average weight(g)=109.7


title: PlimD.05 2

description: PlimD.05 2

tag: Strain Name

source_name: Phosphate limited D=.05

growth_protocol:
limiting nutrient : phosphate
dilution rate : D=0.05


title: NlimD.1

source_name: Nitrate limited D=0.1

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.1


title: Head kidney,vaccine FO-2, pool 2B-rep3

description: Head kidney,vaccine FO-2, pool 2B-rep3

tag: average weight(g)=114.11


title: Head kidney,vaccine FO-2, pool 2A-rep2

description: Head kidney,vaccine FO-2, pool 2A-rep2

label_protocol:
2 μg of pooled total RNA (from 4 fish) were subjected to 1 round of amplification by using the Amino Allyl MessegeAmp II aRNA amplification kit (Ambion)
Coupling of aRNA was done with either Cy3 or Cy5 dye according to the Amino Ally MessageAMP™ II aRNA Amplification Kit (Ambion) protocol with minor modifications. Briefly, one vial of Cy3 or Cy5 reactive dyes (Amersham) was resuspended in 22 µl of DMSO prior to coupling. 3µg of aRNA was dried to completion in a vacuum centrifuge (Savant Instruments, Inc., Farmingdale, NY).  The aRNA was resuspended in 4.5 µl of coupling buffer. Thereafter, 5.5 µl of dye was added to the aRNA:coupling buffer and incubated for 30 min in the dark. 2.25 µl of 4M Hydroxylalamine was then added to quench the reaction followed by 12.75 µl of water to obtain a total volume to 30 µl. Dye labeled aRNA purification was done according to the manufacturer’s instructions.

tag: Bolax strain

tag: average weight(g)=114.10

treatment_protocol: Fish were divided into 4 groups of 50 each by dip netting and sequencial allocation. Two groups (100 fish) were kept in each tank. Marking was done by fin clipping under anaesthesia (0.5ml/L Chlorobutanol (Sigma)). Each fish was intraperitoneally injected with 0.1 ml of experimental water-in-oil vaccines (Pharmaq, Norway).

tag: average side effect score=0.15


title: NlimD.05

source_name: Nitrate limited D=0.054

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.054


title: ClimD.25

source_name: Glucose limited D=0.268

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.268


title: NlimD.2

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-04 Scan Time : 11:49:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Glucose limited D=0.25

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.25

source_name: Nitrate limited D=0.205

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.205


title: ClimD.1

source_name: Glucose limited D=0.109

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.109


title: Head kidney,vaccine FO-2, pool 2A-rep1

description: Head kidney,vaccine FO-2, pool 2A-rep1

tag: average side effect score

tag: average weight(g)=114.9

growth_protocol: Atlantic salmon (Salmo salar) parr were reared in two 500L tanks containing continuously running fresh water at an average temperature of 17 °C. Fish were fed with commercial dry pellets (EWOS, Norway).


title: ClimD.3

source_name: Glucose limited D=0.338

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.338


title: Rice_WBPH_rep2

city: Koshi

first: Masaru

last: Satoh

state: Kumamoto

country: Japan

institute: National Agricultural Research Center for Kyushu Okinawa Region

description: Rice plants at the 5-leaf-stage were encased in transparent plastic cylinders (70 cm x 15 cm) and 20 adult white-backed planthopper (Sogatella furcifera Horváth) males per plant were released in the cylinder. Control plants were put in transparent plastic cylinders without insects. After 24 h, all plants were removed from the cylinders and all insects were removed from the rice plants. Fourth and fifth leaf blades infested with or without insects were collected and frozen in liquid nitrogen. Leaves were collected from three rice plants with or without insects. Then we pooled leaves from multiple plants as the source of RNA. The frozen stored leaves were ground in liquid nitrogen thoroughly with a pestle. Total RNA was extracted from the powder of leaves using Trizol.

hyb_protocol: Kit: in situ hybridization kit plus Manufacturer: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray scanner Manufacturer: Agilent Technologies

data_processing: The TIFF image was used to extract raw and processed data using Agilent’s Feature Extraction software ver 8.1.1.1. Raw result of data processing with Agilent’s Feature Extraction software was provided as Supplementary text file.

organism: Oryza sativa

source_name: Rice leaves, infested with white-backed planthopper (WBPH) for 24 hours.

label_protocol:
Kit: Low input RNA linear amplification kit
Manufacturer: Agilent Technologies

growth_protocol: Rice plants (Oryza sativa L. cv. Hinohikari) were grown from seed planted in plastic pots containing  commercial soil (Hinokunishodo; Japan agricultural Co., Tokyo, Japan). The pots were then submerged in water inside a container and was kept in a glasshouse at 25 ± 1 ℃, 60-80 % RH under natural sunlight.

extract_protocol:
Kit: Trizol
Manufacturer: Invitrogen

treatment_protocol: Rice plants were encased in transparent plastic cylinders (70 cm x 15 cm) and 20 adult white-backed planthopper (Sogatella furcifera Horváth) males per plant were released in the cylinder for 24 h.

tag: Cultivar

value: a Japonica cultivar "Hinohikari"

tag: Leaf-stage

tag: Tissue

value: leaf

source_name: Rice leaves, mock-treated.

treatment_protocol: Rice plants were encased in transparent plastic cylinders (70 cm x 15 cm) without insects for 24 h.


title: Rice_BPH_rep1

description: Rice plants at the 5-leaf-stage were encased in transparent plastic cylinders (70 cm x 15 cm) and 20 adult brown planthopper (Nilaparvata lugens Stål) males per plant were released in the cylinder. Control plants were put in transparent plastic cylinders without insects. After 24 h, all plants were removed from the cylinders and all insects were removed from the rice plants. Fourth and fifth leaf blades infested with or without insects were collected and frozen in liquid nitrogen. Leaves were collected from three rice plants with or without insects. Then we pooled leaves from multiple plants as the source of RNA. The frozen stored leaves were ground in liquid nitrogen thoroughly with a pestle. Total RNA was extracted from the powder of leaves using Trizol.

source_name: Rice leaves, infested with brown planthopper (BPH) for 24 hours.

treatment_protocol: Rice plants were encased in transparent plastic cylinders (70 cm x 15 cm) and 20 adult brown planthopper (Nilaparvata lugens Stål) males per plant were released in the cylinder for 24 h.

tag: Rice plants were encased in transparent plastic cylinders (70 cm x 15 cm) without insects for 24 h.


title: ClimD.15

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 11:37:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Glucose limited D=0.168

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.168


title: Rice_BPH_rep2


title: Rice_BPH_rep3


title: ClimD.05

source_name: Glucose limited D=0.052

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.052


title: Rice_WBPH_rep3

description: Rice plants at the 5-leaf-stage were encased in transparent plastic cylinders (70 cm x 15 cm) and 20 adult white-backed planthopper (Sogatella furcifera Horváth) males per plant were released in the cylinder. Control plants were put in transparent plastic cylinders without insects. After 24 h, all plants were removed from the cylinders and all insects were removed from the rice plants. Fourth and fifth leaf blades infested with or without insects were collected and frozen in liquid nitrogen. The frozen stored leaves were ground in liquid nitrogen thoroughly with a pestle. Total RNA was extracted from the powder of leaves using Trizol.


title: Human GM06990 cells, E2F1 Replicate A

description: Human GM06990 cells

hyb_protocol: Cy-labedled ChIP Samples

source_name: GM06990 cells

tag: E2F1 antibody

tag: control total input


title: Rice_WBPH_rep1

treatment_protocol: Rice plants were encased in transparent plastic cylinders  (70 cm x 15 cm) and 20 adult white-backed planthopper (Sogatella furcifera Horváth) males per plant were released in the cylinder for 24 h.


title: NlimD.15

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-04 Scan Time : 11:41:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Nitrate limited D=0.161

growth_protocol:
limiting nutrient : nitrate
dilution rate : D=0.161


title: Midgut BF 24H rep1

status: Public on Aug 20 2007

city: Irvine

first: Osvaldo

last: Marinotti

address: University of California, Irvine

department: Molecular Biology & Biochemistry

institute: University of California, Irvine

description: A searchable database (Anopheles gambiae Gene Expression Database at UC Irvine) has been made available so that detailed analyses of specific groups of genes based on their descriptions, functions or levels of gene expression variation can be performed. Related publications: Dissanayake, S., Marinotti, O., Ribeiro, J.M.C., & James, A.A. (2006) angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences. BMC Genomics 7:116. & Marinotti, O., Calvo, E., Nguyen, Q. K., Dissanayake, S., Ribeiro, J. M. C., & James, A. A. (2006) Genome-wide analysis of gene expression in adult Anopheles gambiae. Insect Mol Biol 15 (1), 1-12. Marinotti, O., Nguyen, Q. K., Calvo, E., James, A. A., & Ribeiro, J. M. C. (2005) Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae. Insect Mol Biol 14 (4), 365-373.

hyb_protocol: 10 µg of this fragmented target cRNA was hybridized at 45 °C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip® Plasmodium/Anopheles Genome Array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000. The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.).

data_processing: The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values).

label: biotin

organism: Anopheles gambiae

source_name: Midgut at 24 hours post-bloodmeal

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly (A)+ mRNA present in the isolated total RNA (10 µg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA, USA) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds-cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA). 15 µg of the resulting biotin-tagged cRNA were fragmented to strands of 35–200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

growth_protocol: Larvae were fed on finely powdered fish food (Tetramind, Tetra Werke, Germany) mixed 1:1 with yeast powder. Adults (males and females) were kept in cages with access ad libitum to raisins and water. For blood feeding, adult female mosquitoes were fed on mice anaesthetized with a mixture of ketamine and xylazine. Males and females were kept together in the cage until the blood meal. Blood-fed females were transferred to a separate cage and kept without males for the remaining duration of the experiment. The transferred females were kept with access to raisins and water and were offered a cup with water as oviposition site at all times. Egg laying was observed between 72 and 96 h PBM. Three samples composed of five mosquitoes each were collected for each experimental time point, the RNA was immediately extracted and stored at -80°C.

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD, USA) and purified further by passing it through an RNeasy spin column (Qiagen, Chatsworth, CA, USA). Eluted total RNAs were quantified and a portion of the recovered material adjusted to a final concentration of 1 µg/µl. All starting total RNA samples were quality-assessed prior to beginning target preparation/processing steps by resolving a small amount of each sample (typically 25–250 ng/well) on to a RNA Laboratory-On-A-Chip (Caliper Technologies, Mountain View, CA, USA) that was evaluated on an Agilent Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Animals were maintained at 25°C, 75–85% relative humidity and a 18/6 h light/dark cycle.


title: Ovaries BF 24H rep1

source_name: Ovaries at 24 hours post-bloodmeal


title: Male rep3

source_name: Whole male mosquito 3 days post-emergence


title: Fat bodies BF 24H rep3

source_name: Fat bodies at 24 hours post-bloodmeal


title: Fat bodies BF 24H rep2


title: Ovaries BF 24H rep3


title: Midgut BF 24H rep3


title: Male rep2


title: Larvae rep1

source_name: Larvae 3rd and 4th instars


title: Larvae rep2


title: Whole BF 96H rep1

source_name: Whole mosquito 96 hours post-bloodmeal


title: Whole BF 96H rep3


title: Midgut BF 24H rep2


title: Larvae rep3


title: Whole NBF rep2

source_name: Whole female mosquito sugar-fed 3 days post-emergence


title: Ovaries BF 24H rep2


title: Whole NBF rep3


title: Whole NBF rep1


title: Whole BF 96H rep2


title: Whole BF 15D rep2

source_name: Whole mosquito 15 days post-bloodmeal


title: Whole BF 15D rep1


title: Fat bodies BF 24H rep1


title: Whole BF 72H rep1

source_name: Whole mosquito 72 hours post-bloodmeal


title: Whole BF 15D rep3


title: Male rep1


title: Whole BF 48H rep3

source_name: Whole mosquito 48 hours post-bloodmeal


title: Whole BF 72H rep2


title: Whole BF 48H rep1


title: Whole BF 24H rep3

source_name: Whole mosquito 24 hours post-bloodmeal


title: Whole BF 24H rep2


title: Whole BF 3H rep1

source_name: Whole mosquito 3 hours post-bloodmeal


title: Whole BF 3H rep2


title: Whole BF 24H rep1


title: Whole BF 48H rep2


title: Whole BF 3H rep3


title: Whole BF 72H rep3


title: Head kidney,vaccine FO-2, pool 2C-rep6

description: Head kidney,vaccine FO-2, pool 2C-rep6

hyb_protocol: Post-print processing of arrays was done by washing 2 X 5 min in 0.2% SDS, 5 X 1 min in MilliQ water followed by immersion in MilliQ water at 100 °C for 3 min. The slides were dried by centrifugation at 512 X g for 5 min.Prehybridization involved placing the arrays in (5 X SSC, 1% SDS and 3% BSA (Sigma)) and incubating at 49 °C in a water bath for 1½ hrs. Thereafter, the arrays were washed thrice for 20 sec in MilliQ water and dried by centrifugation as above. For hybridization, 500 ng of labeled target reconstituted to a final volume of 26 µL, 30 µL of 2X formamide hybridization buffer (Genisphere) and 4 µL LNT dT blocker (Genisphere) were used. Hybridization was done at 49 °C in a water bath for 16 hrs. The arrays were washed first in (2X SSC, 0.1% SDS) for 10 min at 49 °C, 2 X 5min in (2X SSC, 0.1% SDS) at room temperature, 2 X 5 min in 1X SSC, 4 X 5 min in 0.1X SSC followed immediately by centrifugation at 512 X g for 5 min.

scan_protocol: Imaging was done at 10 µm resolution using ScanArray™ Express microarray scanner (Packard Bioscience). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively, at the same laser power (90%), with adjusted photomultiplier tube settings between slides to balance the Cy5 and Cy3 channels. Image analysis and fluorescent intensity data was extracted from Tiff images using ImaGene™ 5.6 Standard Edition softwareScanning was done using ScanArray™ Express microarray skanner

source_name: Total RNA from head kidney at 12 weeks post vaccination

tag: Fish vaccinated with A. salmonicida (6x standard antigen concentration)

tag: average injection site inflammatory score=0.59

tag: average weight(g)=114.14

tag: Fish vaccinated with A. salmonicida (standard antigen concentration)

tag: average side effect score= 0.15


title: Ras* gal 0min vs. 40min - 2

status: Public on Aug 18 2007

first: Cemile

middle: Gokce

last: Guldal

address: Washington Road, Lewis Thomas Lab

department: Molecular Biology

description: Ras* gal 0min vs. 40min - 2

hyb_protocol: Hybridization date : 1/29/2005 Two-Color Microarray-Based Gene Expression Analysis v.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 10:33:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Ras* gal 0min

label_protocol:
Type of label : Cy3
Two-Color Microarray-Based Gene Expression Analysis v.5.5

growth_protocol: media : galactose

extract_protocol:
Extraction description : mechanical distruption
Extraction method : Qiagen Rneasy Kit

treatment_protocol: Time : 0min

tag: Strain Name

source_name: Ras* gal 40min

label_protocol:
Type of label : Cy5
Two-Color Microarray-Based Gene Expression Analysis v.5.5

treatment_protocol: Time : 40min


title: WT glu 0min vs. 60min - 2

description: WT glu 0min vs. 60min - 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 11:32:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: WT glu 0min

growth_protocol: media : glucose

source_name: WT glu 60min

treatment_protocol: Time : 60min


title: Ras*tpkw gal 0min vs. 20min - 2

description: Ras*tpkw gal 0min vs. 20min - 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 11:17:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Ras*tpkw gal 0min

source_name: Ras*tpkw gal 20min

treatment_protocol: Time : 20min


title: WT gal 0min vs. 60min

description: WT gal 0min vs. 60min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 11:40:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: WT gal 0min

source_name: WT gal 60min


title: Ras* gal 0min vs. 60min

description: Ras* gal 0min vs. 60min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 11:48:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Ras* gal 60min


title: Ras*tpkw gal 0min vs. 60min - 2

description: Ras*tpkw gal 0min vs. 60min - 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 10:17:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Ras*tpkw gal 60min


title: Ras* gal 0min vs. 40min

description: Ras* gal 0min vs. 40min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 12:08:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Ras* gal 0min vs. 20min - 2

description: Ras* gal 0min vs. 20min - 2

source_name: Ras* gal 20min


title: WT gal 0min vs. 60min - 2

description: WT gal 0min vs. 60min - 2


title: Ras*tpkw gal 0min vs. 40min

description: Ras*tpkw gal 0min vs. 40min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 10:25:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Ras*tpkw gal 40min


title: Ras*tpkw gal 0min vs. 40min - 2

description: Ras*tpkw gal 0min vs. 40min - 2


title: WT glu 0min vs. 40min - 2

description: WT glu 0min vs. 40min - 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 09:58:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: WT glu 40min


title: Ras*tpkw gal 0min vs. 60min

description: Ras*tpkw gal 0min vs. 60min


title: WT gal 0min vs. 20min - 2

description: WT gal 0min vs. 20min - 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 09:34:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: WT gal 20min


title: WT glu 0min vs. 20min - 2

description: WT glu 0min vs. 20min - 2

source_name: WT glu 20min


title: Ras*tpkw gal 0min vs. 20min

description: Ras*tpkw gal 0min vs. 20min


title: ClimD.2

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-01 Scan Time : 12:16:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Glucose limited D=0.25

source_name: Glucose limited D=0.224

growth_protocol:
limiting nutrient : glucose
dilution rate : D=0.224


title: WT glu 0min vs. 20min

description: WT glu 0min vs. 20min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 09:50:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: WT gal 0min vs. 40min - 2

description: WT gal 0min vs. 40min - 2

source_name: WT gal 40min


title: WT glu 0min vs. 60min

description: WT glu 0min vs. 60min


title: Ras* gal 0min vs. 60min - 2

description: Ras* gal 0min vs. 60min - 2

source_name: Ras* gal 0min


title: Ras* gal 0min vs. 20min

description: Ras* gal 0min vs. 20min


title: WT gal 0min vs. 40min

description: WT gal 0min vs. 40min

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-27 Scan Time : 09:42:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: tpk-w gal 0min vs. 40min

description: tpk-w gal 0min vs. 40min

hyb_protocol: Hybridization date : 3/3/2005 Two-Color Microarray-Based Gene Expression Analysis v.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:54:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: tpk-w gal 0min

source_name: tpk-w gal 40min


title: WT glu 0min vs. 40min

description: WT glu 0min vs. 40min

source_name: WT glu 0min


title: tpk-w gal 0min vs. 20min

description: tpk-w gal 0min vs. 20min

source_name: tpk-w gal 20min


title: tpk-w gal 0min vs. tpk-w gal 40min

description: tpk-w gal 0min vs. tpk-w gal 40min

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:38:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Streptococcus pneumoniae serotype 2 strain D39 Slide54

status: Public on Aug 17 2007

city: Adelaide

first: Uwe

last: Stroeher

state: South Australia

address: North Terrace

department: School of Molecular and Biomedical Science

country: Australia

institute: University of Adelaide

description: An analysis of the transcriptome of the two phases of Streptococcus pneumoniae

hyb_protocol: Hybridization carried out at 65C in buffer containing formamide, SSC and SDS

scan_protocol: Axon GenePix 4000B scanner

data_processing: SPOT software

organism: Streptococcus pneumoniae

source_name: Total RNA Transparent variant

label_protocol: cDNA was derived from mRNA and labelled indirectly using amino ally dUTP

growth_protocol: Bacteria grown to optical density of 0.45 at absorbance at 600nm in Todd Hewitt Broth

extract_protocol: Total RNA was extracted using hot acid phenol

tag: Serotpye 2 strain D39

source_name: Total RNA Opaque variant


title: Streptococcus pneumoniae serotype 2 strain D39 Slide55


title: WT gal 0min vs. WT gal 20min

description: WT gal 0min vs. WT gal 20min

source_name: WT gal 0min


title: tpk-w gal 0min vs. 60min

description: tpk-w gal 0min vs. 60min

scan_protocol: Pixel Size : 10 Scan Date : 2005-03-03 Scan Time : 12:46:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: tpk-w gal 60min


title: Streptococcus pneumoniae serotype 2 strain D39 Slide42


title: Streptococcus pneumoniae serotype 2 strain D39 Slide47


title: Streptococcus pneumoniae serotype 2 strain D39 Slide41


title: Streptococcus pneumoniae serotype 2 strain D39 Slide51


title: Streptococcus pneumoniae serotype 2 strain D39 Slide52


title: Streptococcus pneumoniae serotype 2 strain D39 Slide50


title: Breast Cancer Cell-line ZR-75-1

status: Public on Aug 16 2007

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: No additional information

hyb_protocol: Hybridisation protocol available via the VUMC MACF website. Also described in van den Ijssel et al, NAR 2005 Dec 16; 33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies) default settings

data_processing: Spot analysis and QC was fully automated using BlueFuse version 3.1 (BlueGnome, Cambrdige UK); mode-normalisation.

source_name: genomic DNA from breast cell-lineZR-75-1

label_protocol: DNA labelling protocol available via the VUMC MACF website. Also described in van den Ijssel et al, NAR 2005 Dec 16; 33(22):e192

extract_protocol: Proteinase K/SDS (according to Maniatis)

tag: Breast Cancer Cell Line (Female)

source_name: genomic DNA from male reference DNA

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


title: WT gal 0min vs. 20min

description: WT gal 0min vs. 20min


title: Streptococcus pneumoniae serotype 2 strain D39 Slide40


title: Breast Cancer Cell-line ZR-75-30

description: No additional information

source_name: genomic DNA from breast cell-lineZR-75-30


title: Breast Cancer Cell-line VP267

description: No additional information

source_name: genomic DNA from breast cell-lineVP267


title: Breast Cancer Cell-line SUM52

description: No additional information

source_name: genomic DNA from breast cell-lineSUM52


title: Breast Cancer Cell-line VP185

description: No additional information

source_name: genomic DNA from breast cell-lineVP185


title: Breast Cancer Cell-line SUM44

description: No additional information

source_name: genomic DNA from breast cell-lineSUM44


title: Breast Cancer Cell-line VP303

description: No additional information

source_name: genomic DNA from breast cell-lineVP303


title: Streptococcus pneumoniae serotype 2 strain D39 Slide49


title: Breast Cancer Cell-line SUM102

description: No additional information

source_name: genomic DNA from breast cell-lineSUM102


title: Breast Cancer Cell-line SUM1315

description: No additional information

source_name: genomic DNA from breast cell-lineSUM1315


title: Breast Cancer Cell-line SUM190

description: No additional information

source_name: genomic DNA from breast cell-lineSUM190


title: Breast Cancer Cell-line OCUB-M

description: No additional information

source_name: genomic DNA from breast cell-lineOCUB-M


title: Breast Cancer Cell-line UACC812

description: No additional information

source_name: genomic DNA from breast cell-lineUACC812


title: Breast Cancer Cell-line VP229

description: No additional information

source_name: genomic DNA from breast cell-lineVP229


title: Breast Cancer Cell-line HCC1599

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1599


title: Breast Cancer Cell-line SUM159

description: No additional information

source_name: genomic DNA from breast cell-lineSUM159


title: Breast Cancer Cell-line SKBR3

description: No additional information

source_name: genomic DNA from breast cell-lineSKBR3


title: Breast Cancer Cell-line BT474

description: No additional information

source_name: genomic DNA from breast cell-lineBT474


title: Breast Cancer Cell-line PMC42

description: No additional information

source_name: genomic DNA from breast cell-linePMC42

source_name: genomic DNA from male reference DNA


title: Breast Cancer Cell-line MDA175

description: No additional information

source_name: genomic DNA from breast cell-lineMDA175


title: Breast Cancer Cell-line SKBR7

description: No additional information

source_name: genomic DNA from breast cell-lineSKBR7


title: Breast Cancer Cell-line MDA436

description: No additional information

source_name: genomic DNA from breast cell-lineMDA436


title: Breast Cancer Cell-line MDA157

description: No additional information

source_name: genomic DNA from breast cell-lineMDA157


title: Breast Cancer Cell-line MDA453

description: No additional information

source_name: genomic DNA from breast cell-lineMDA453


title: Breast Cancer Cell-line SUM149

description: No additional information

source_name: genomic DNA from breast cell-lineSUM149


title: Breast Cancer Cell-line MDA468

description: No additional information

source_name: genomic DNA from breast cell-lineMDA468


title: Breast Cancer Cell-line MT3

description: No additional information

source_name: genomic DNA from breast cell-lineMT3


title: Breast Cancer Cell-line KPL-1

description: No additional information

source_name: genomic DNA from breast cell-lineKPL-1


title: Breast Cancer Cell-line BT549

description: No additional information

source_name: genomic DNA from breast cell-lineBT549


title: Breast Cancer Cell-line T47D

description: No additional information

source_name: genomic DNA from breast cell-lineT47D


title: Breast Cancer Cell-line MDA415

description: No additional information

source_name: genomic DNA from breast cell-lineMDA415


title: Breast Cancer Cell-line IBEP-1

description: No additional information

source_name: genomic DNA from breast cell-lineIBEP-1


title: Breast Cancer Cell-line OCUB-F

description: No additional information

source_name: genomic DNA from breast cell-lineOCUB-F


title: Breast Cancer Cell-line MDA361

description: No additional information

source_name: genomic DNA from breast cell-lineMDA361


title: Breast Cancer Cell-line Hs578t

description: No additional information

source_name: genomic DNA from breast cell-lineHs578t


title: Breast Cancer Cell-line MDA134

description: No additional information

source_name: genomic DNA from breast cell-lineMDA134

source_name: genomic DNA from male reference DNA


title: Breast Cancer Cell-line HCC38

description: No additional information

source_name: genomic DNA from breast cell-lineHCC38


title: Breast Cancer Cell-line HCC70

description: No additional information

source_name: genomic DNA from breast cell-lineHCC70


title: Breast Cancer Cell-line HCC1569

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1569


title: Breast Cancer Cell-line HCC1937

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1937


title: Breast Cancer Cell-line HCC1187

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1187


title: Breast Cancer Cell-line HCC1419

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1419


title: Breast Cancer Cell-line HCC1395

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1395


title: Breast Cancer Cell-line DU4475

description: No additional information

source_name: genomic DNA from breast cell-lineDU4475


title: Breast Cancer Cell-line GI-101

description: No additional information

source_name: genomic DNA from breast cell-lineGI-101


title: Breast Cancer Cell-line HCC1500

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1500


title: Primary Breast Tumor 2504

description: No additional information

source_name: genomic DNA from primary breast tumor2504

tag: Primary breast tumour (Female)

tag: Male Reference DNA


title: Breast Cancer Cell-line HCC1143

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1143


title: Primary Breast Tumor 2483

description: No additional information

source_name: genomic DNA from primary breast tumor2483


title: Primary Breast Tumor 2499

description: No additional information

source_name: genomic DNA from primary breast tumor2499


title: Breast Cancer Cell-line HCC1954

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1954


title: Primary Breast Tumor 2492

description: No additional information

source_name: genomic DNA from primary breast tumor2492


title: Primary Breast Tumor 2498

description: No additional information

source_name: genomic DNA from primary breast tumor2498

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2496

description: No additional information

source_name: genomic DNA from primary breast tumor2496


title: Primary Breast Tumor 2461

description: No additional information

source_name: genomic DNA from primary breast tumor2461


title: Primary Breast Tumor 2462

description: No additional information

source_name: genomic DNA from primary breast tumor2462


title: Breast Cancer Cell-line HCC1806

description: No additional information

source_name: genomic DNA from breast cell-lineHCC1806


title: Primary Breast Tumor 2479

description: No additional information

source_name: genomic DNA from primary breast tumor2479


title: Breast Cancer Cell-line CAL51

description: No additional information

source_name: genomic DNA from breast cell-lineCAL51


title: Primary Breast Tumor 2505

description: No additional information

source_name: genomic DNA from primary breast tumor2505


title: Primary Breast Tumor 2484

description: No additional information

source_name: genomic DNA from primary breast tumor2484


title: Primary Breast Tumor 2474

description: No additional information

source_name: genomic DNA from primary breast tumor2474


title: Primary Breast Tumor 2468

description: No additional information

source_name: genomic DNA from primary breast tumor2468


title: Primary Breast Tumor 2460

description: No additional information

source_name: genomic DNA from primary breast tumor2460


title: Primary Breast Tumor 2453

description: No additional information

source_name: genomic DNA from primary breast tumor2453


title: Primary Breast Tumor 2456

description: No additional information

source_name: genomic DNA from primary breast tumor2456


title: Primary Breast Tumor 2438

description: No additional information

source_name: genomic DNA from primary breast tumor2438


title: Primary Breast Tumor 2446

description: No additional information

source_name: genomic DNA from primary breast tumor2446


title: Primary Breast Tumor 2444

description: No additional information

source_name: genomic DNA from primary breast tumor2444


title: Primary Breast Tumor 2426

description: No additional information

source_name: genomic DNA from primary breast tumor2426

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2406

description: No additional information

source_name: genomic DNA from primary breast tumor2406


title: Primary Breast Tumor 2420

description: No additional information

source_name: genomic DNA from primary breast tumor2420


title: Primary Breast Tumor 2405

description: No additional information

source_name: genomic DNA from primary breast tumor2405


title: Primary Breast Tumor 2393

description: No additional information

source_name: genomic DNA from primary breast tumor2393


title: Primary Breast Tumor 2410

description: No additional information

source_name: genomic DNA from primary breast tumor2410


title: Primary Breast Tumor 2436

description: No additional information

source_name: genomic DNA from primary breast tumor2436


title: Primary Breast Tumor 2416

description: No additional information

source_name: genomic DNA from primary breast tumor2416


title: Primary Breast Tumor 2421

description: No additional information

source_name: genomic DNA from primary breast tumor2421


title: Primary Breast Tumor 2419

description: No additional information

source_name: genomic DNA from primary breast tumor2419


title: Primary Breast Tumor 2401

description: No additional information

source_name: genomic DNA from primary breast tumor2401


title: Primary Breast Tumor 2380

description: No additional information

source_name: genomic DNA from primary breast tumor2380


title: Primary Breast Tumor 2386

description: No additional information

source_name: genomic DNA from primary breast tumor2386


title: Primary Breast Tumor 2412

description: No additional information

source_name: genomic DNA from primary breast tumor2412


title: Primary Breast Tumor 2378

description: No additional information

source_name: genomic DNA from primary breast tumor2378


title: Primary Breast Tumor 2374

description: No additional information

source_name: genomic DNA from primary breast tumor2374


title: Primary Breast Tumor 2375

description: No additional information

source_name: genomic DNA from primary breast tumor2375


title: Primary Breast Tumor 2360

description: No additional information

source_name: genomic DNA from primary breast tumor2360

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2377

description: No additional information

source_name: genomic DNA from primary breast tumor2377


title: Primary Breast Tumor 2353

description: No additional information

source_name: genomic DNA from primary breast tumor2353


title: Primary Breast Tumor 2358

description: No additional information

source_name: genomic DNA from primary breast tumor2358


title: Primary Breast Tumor 2402

description: No additional information

source_name: genomic DNA from primary breast tumor2402


title: Primary Breast Tumor 2351

description: No additional information

source_name: genomic DNA from primary breast tumor2351


title: Primary Breast Tumor 2356

description: No additional information

source_name: genomic DNA from primary breast tumor2356


title: Primary Breast Tumor 2372

description: No additional information

source_name: genomic DNA from primary breast tumor2372


title: Primary Breast Tumor 2355

description: No additional information

source_name: genomic DNA from primary breast tumor2355


title: Primary Breast Tumor 2342

description: No additional information

source_name: genomic DNA from primary breast tumor2342


title: Primary Breast Tumor 2348

description: No additional information

source_name: genomic DNA from primary breast tumor2348


title: Primary Breast Tumor 2349

description: No additional information

source_name: genomic DNA from primary breast tumor2349


title: Primary Breast Tumor 2350

description: No additional information

source_name: genomic DNA from primary breast tumor2350


title: Primary Breast Tumor 2341

description: No additional information

source_name: genomic DNA from primary breast tumor2341


title: Primary Breast Tumor 2337

description: No additional information

source_name: genomic DNA from primary breast tumor2337


title: Primary Breast Tumor 2327

description: No additional information

source_name: genomic DNA from primary breast tumor2327


title: Primary Breast Tumor 2334

description: No additional information

source_name: genomic DNA from primary breast tumor2334


title: Primary Breast Tumor 2347

description: No additional information

source_name: genomic DNA from primary breast tumor2347

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2333

description: No additional information

source_name: genomic DNA from primary breast tumor2333


title: Primary Breast Tumor 2345

description: No additional information

source_name: genomic DNA from primary breast tumor2345


title: Primary Breast Tumor 2323

description: No additional information

source_name: genomic DNA from primary breast tumor2323


title: Primary Breast Tumor 2317

description: No additional information

source_name: genomic DNA from primary breast tumor2317


title: Primary Breast Tumor 2325

description: No additional information

source_name: genomic DNA from primary breast tumor2325


title: Primary Breast Tumor 2324

description: No additional information

source_name: genomic DNA from primary breast tumor2324


title: Primary Breast Tumor 2312

description: No additional information

source_name: genomic DNA from primary breast tumor2312


title: Primary Breast Tumor 2309

description: No additional information

source_name: genomic DNA from primary breast tumor2309


title: Primary Breast Tumor 2297

description: No additional information

source_name: genomic DNA from primary breast tumor2297


title: Primary Breast Tumor 2310

description: No additional information

source_name: genomic DNA from primary breast tumor2310


title: Primary Breast Tumor 2313

description: No additional information

source_name: genomic DNA from primary breast tumor2313


title: Primary Breast Tumor 2294

description: No additional information

source_name: genomic DNA from primary breast tumor2294


title: Primary Breast Tumor 2305

description: No additional information

source_name: genomic DNA from primary breast tumor2305


title: Primary Breast Tumor 2290

description: No additional information

source_name: genomic DNA from primary breast tumor2290


title: Primary Breast Tumor 2293

description: No additional information

source_name: genomic DNA from primary breast tumor2293


title: Primary Breast Tumor 2289

description: No additional information

source_name: genomic DNA from primary breast tumor2289


title: Primary Breast Tumor 2302

description: No additional information

source_name: genomic DNA from primary breast tumor2302

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2268

description: No additional information

source_name: genomic DNA from primary breast tumor2268


title: Primary Breast Tumor 2308

description: No additional information

source_name: genomic DNA from primary breast tumor2308


title: Primary Breast Tumor 2287

description: No additional information

source_name: genomic DNA from primary breast tumor2287


title: Primary Breast Tumor 2286

description: No additional information

source_name: genomic DNA from primary breast tumor2286


title: Primary Breast Tumor 2270

description: No additional information

source_name: genomic DNA from primary breast tumor2270


title: Primary Breast Tumor 2246

description: No additional information

source_name: genomic DNA from primary breast tumor2246


title: Primary Breast Tumor 2254

description: No additional information

source_name: genomic DNA from primary breast tumor2254


title: Primary Breast Tumor 2250

description: No additional information

source_name: genomic DNA from primary breast tumor2250


title: Primary Breast Tumor 2241

description: No additional information

source_name: genomic DNA from primary breast tumor2241


title: Primary Breast Tumor 2231

description: No additional information

source_name: genomic DNA from primary breast tumor2231


title: Primary Breast Tumor 2239

description: No additional information

source_name: genomic DNA from primary breast tumor2239


title: Primary Breast Tumor 2237

description: No additional information

source_name: genomic DNA from primary breast tumor2237


title: Primary Breast Tumor 2227

description: No additional information

source_name: genomic DNA from primary breast tumor2227


title: Primary Breast Tumor 2282

description: No additional information

source_name: genomic DNA from primary breast tumor2282


title: Primary Breast Tumor 2233

description: No additional information

source_name: genomic DNA from primary breast tumor2233


title: Primary Breast Tumor 2228

description: No additional information

source_name: genomic DNA from primary breast tumor2228


title: Primary Breast Tumor 2230

description: No additional information

source_name: genomic DNA from primary breast tumor2230

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2229

description: No additional information

source_name: genomic DNA from primary breast tumor2229


title: Primary Breast Tumor 2222

description: No additional information

source_name: genomic DNA from primary breast tumor2222


title: Primary Breast Tumor 2219

description: No additional information

source_name: genomic DNA from primary breast tumor2219


title: Primary Breast Tumor 2220

description: No additional information

source_name: genomic DNA from primary breast tumor2220


title: Primary Breast Tumor 2236

description: No additional information

source_name: genomic DNA from primary breast tumor2236


title: Primary Breast Tumor 2225

description: No additional information

source_name: genomic DNA from primary breast tumor2225


title: Primary Breast Tumor 2211

description: No additional information

source_name: genomic DNA from primary breast tumor2211


title: Primary Breast Tumor 2252

description: No additional information

source_name: genomic DNA from primary breast tumor2252


title: Primary Breast Tumor 2206

description: No additional information

source_name: genomic DNA from primary breast tumor2206


title: Primary Breast Tumor 2210

description: No additional information

source_name: genomic DNA from primary breast tumor2210


title: Primary Breast Tumor 2218

description: No additional information

source_name: genomic DNA from primary breast tumor2218


title: Primary Breast Tumor 2204

description: No additional information

source_name: genomic DNA from primary breast tumor2204


title: Primary Breast Tumor 2200

description: No additional information

source_name: genomic DNA from primary breast tumor2200


title: Primary Breast Tumor 2199

description: No additional information

source_name: genomic DNA from primary breast tumor2199


title: Primary Breast Tumor 2202

description: No additional information

source_name: genomic DNA from primary breast tumor2202


title: Primary Breast Tumor 2183

description: No additional information

source_name: genomic DNA from primary breast tumor2183


title: Primary Breast Tumor 2217

description: No additional information

source_name: genomic DNA from primary breast tumor2217

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2201

description: No additional information

source_name: genomic DNA from primary breast tumor2201


title: Primary Breast Tumor 2207

description: No additional information

source_name: genomic DNA from primary breast tumor2207


title: Primary Breast Tumor 2209

description: No additional information

source_name: genomic DNA from primary breast tumor2209


title: Primary Breast Tumor 2185

description: No additional information

source_name: genomic DNA from primary breast tumor2185


title: Primary Breast Tumor 2198

description: No additional information

source_name: genomic DNA from primary breast tumor2198


title: Primary Breast Tumor 2180

description: No additional information

source_name: genomic DNA from primary breast tumor2180


title: Primary Breast Tumor 2191

description: No additional information

source_name: genomic DNA from primary breast tumor2191


title: Primary Breast Tumor 2166

description: No additional information

source_name: genomic DNA from primary breast tumor2166


title: Primary Breast Tumor 2197

description: No additional information

source_name: genomic DNA from primary breast tumor2197


title: Primary Breast Tumor 2162

description: No additional information

source_name: genomic DNA from primary breast tumor2162


title: Primary Breast Tumor 2176

description: No additional information

source_name: genomic DNA from primary breast tumor2176


title: Primary Breast Tumor 2171

description: No additional information

source_name: genomic DNA from primary breast tumor2171


title: Primary Breast Tumor 2177

description: No additional information

source_name: genomic DNA from primary breast tumor2177


title: Primary Breast Tumor 2172

description: No additional information

source_name: genomic DNA from primary breast tumor2172


title: Primary Breast Tumor 2167

description: No additional information

source_name: genomic DNA from primary breast tumor2167


title: Primary Breast Tumor 2159

description: No additional information

source_name: genomic DNA from primary breast tumor2159


title: Primary Breast Tumor 2163

description: No additional information

source_name: genomic DNA from primary breast tumor2163

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2196

description: No additional information

source_name: genomic DNA from primary breast tumor2196


title: Primary Breast Tumor 2184

description: No additional information

source_name: genomic DNA from primary breast tumor2184


title: Primary Breast Tumor 2174

description: No additional information

source_name: genomic DNA from primary breast tumor2174


title: Primary Breast Tumor 2186

description: No additional information

source_name: genomic DNA from primary breast tumor2186


title: Primary Breast Tumor 2160

description: No additional information

source_name: genomic DNA from primary breast tumor2160


title: Primary Breast Tumor 2181

description: No additional information

source_name: genomic DNA from primary breast tumor2181


title: Primary Breast Tumor 2157

description: No additional information

source_name: genomic DNA from primary breast tumor2157


title: Primary Breast Tumor 2203

description: No additional information

source_name: genomic DNA from primary breast tumor2203


title: Primary Breast Tumor 2149

description: No additional information

source_name: genomic DNA from primary breast tumor2149


title: Primary Breast Tumor 2145

description: No additional information

source_name: genomic DNA from primary breast tumor2145


title: Primary Breast Tumor 2113

description: No additional information

source_name: genomic DNA from primary breast tumor2113


title: Primary Breast Tumor 2156

description: No additional information

source_name: genomic DNA from primary breast tumor2156


title: Primary Breast Tumor 2104

description: No additional information

source_name: genomic DNA from primary breast tumor2104


title: Primary Breast Tumor 2109

description: No additional information

source_name: genomic DNA from primary breast tumor2109


title: Primary Breast Tumor 2108

description: No additional information

source_name: genomic DNA from primary breast tumor2108


title: Primary Breast Tumor 2142

description: No additional information

source_name: genomic DNA from primary breast tumor2142


title: Primary Breast Tumor 2131

description: No additional information

source_name: genomic DNA from primary breast tumor2131

source_name: genomic DNA from male reference DNA


title: Primary Breast Tumor 2146

description: No additional information

source_name: genomic DNA from primary breast tumor2146


title: Primary Breast Tumor 2125

description: No additional information

source_name: genomic DNA from primary breast tumor2125


title: Primary Breast Tumor 2099

description: No additional information

source_name: genomic DNA from primary breast tumor2099


title: Primary Breast Tumor 2111

description: No additional information

source_name: genomic DNA from primary breast tumor2111