title: Cervical carcinoma cell line (VUMC_SiHa_b2s58)

status: Public on Jun 25 2008

type: RNA

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: HPV 16 containing cervical carcinoma cell line, endogenous hTERT positive

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

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

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. Microarray data were normalised using Lowess regression. When both intensities were below 50, hybridisation was assumed inefficient and the ratio value was considered ‘missing’. The cut-off “50” is based on technical reproducibility: intensities above 50 were reasonably reproducible for technical replicates on our platform. To obtain more stable ratios, intensity values below 50 were substituted by 50 when the other channel was above 50.

molecule: total RNA

organism: Homo sapiens

source_name: cervix

label_protocol: cDNA was prepared from 75 micrograms of total RNA using oligo-dT20-VN primer (Invitrogen) and coupled to Cy3 by enzymatic labelling with dUTP-Cy3

extract_protocol: TRIzol according to manufacturers' instructions

tag: cervical carcinoma cell line

source_name: universal human reference RNA (Stratagene)

label_protocol: as ch1, Cy5 in stead of Cy3

extract_protocol: see the Stratagene web site

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


title: HPV 16 immortalized keratinocytes (VUMC_MCF15cl15b_b2s66)

description: HPV 16 immortalized keratinocytes with chromosome 6, endogenous hTERT positive

source_name: foreskin

tag: HPV 16 immortalized keratinocytes


title: HPV 16 immortalized keratinocytes (VUMC_MCF15cl21_b2s59)


title: HPV 16 immortalized keratinocytes (VUMC_MCF29cl8_b2s72)

description: HPV 16 immortalized keratinocytes with ectopic hTERT and chromosome 6, endogenous hTERT negative


title: HPV 16 immortalized keratinocytes (VUMC_MCF9cl6b_b2s55)


title: Primary keratinocytes (VUMC_EK2000-12_b2s78)

description: primary keratinocytes, endogenous hTERT negative

tag: primary keratinocytes


title: S27_L

status: Public on Jun 19 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage.  Total RNA was isolated from nine replications of B73, Mo17, and F1 maize seedling genotypes (6 individual seedlings pooled for each genotype in each replication) using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol.  Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer’s protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridize to the GP2613 platform.

hyb_protocol: Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (27 total) was scanned a minimum of six times in ascending amounts of laser power and PMT gain settings. Slides 1-15 were scanned using the ScanArray5000 (Packard, Meriden, CA).  Slides 16-27 were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA).  Two scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications.  Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Zea mays

source_name: Seedling stage above ground tissue

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.   Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

extract_protocol: total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer’s instructions

tag: Genotype:	B73

tag: Tissue

value: above ground seedling

tag: Dev stage

value: 14 days old

tag: Sample name:	P12 B73 Cy3

tag: Genotype:	F1

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P12 F1 Cy5


title: Primary keratinocytes (VUMC_EK2000-13_b2s57)

description: primary keratinocytes, enodgenous hTERT negative


title: HPV 16 immortalized keratinocytes (VUMC_MCF9cl19_b2s79)


title: HPV 16 immortalized keratinocytes (VUMC_MCF15cl18_b2s54)


title: S24_L

tag: Sample name:	P11 B73 Cy3

tag: Genotype:	Mo17

tag: Sample name:	P11 Mo17 Cy5


title: HPV 16 immortalized keratinocytes (VUMC_MCF9cl6_b2s61)


title: HPV 16 immortalized keratinocytes (VUMC_MCF15cl8_b2s74)


title: HPV 16 immortalized keratinocytes (VUMC_MCF26cl4_b2s63)


title: HPV 16 immortalized keratinocytes (VUMC_MCF25cl2_b2s67)


title: HPV 16 immortalized keratinocytes (VUMC_MCF15cl20_b2s62)


title: S20_L

tag: Sample name:	P8 B73 Cy3

tag: Sample name:	P8 Mo17 Cy5


title: HPV 16 immortalized keratinocytes (VUMC_FK16AhTERT_b2s73)

description: HPV 16 immortalized primary keratinocytes with ectopic hTERT, endogenous hTERT positive


title: S26_L

tag: Sample name:	P12 Mo17 Cy3

tag: Sample name:	P12 B73 Cy5


title: S19_L

tag: Sample name:	P7 F1 Cy3

tag: Sample name:	P7 B73 Cy5


title: S21_L

tag: Sample name:	P8 Mo17 Cy3

tag: Sample name:	P8 F1 Cy5


title: HPV 16 immortalized keratinocytes (VUMC_FK16A_b2s57)

description: HPV 16 immortalized keratinocytes, enodgenous hTERT positive

tag: HPV 16 immortalized keratinocytes

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


title: S15_L

tag: Genotype:	B73

tag: Tissue

tag: Dev stage

tag: Sample name:	P6 B73 Cy3

tag: Genotype:	F1

tag: Sample name:	P6 F1 Cy5


title: S23_L

tag: Sample name:	P11 F1 Cy3

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P11 B73 Cy5


title: S6_L

tag: Sample name:	P3 F1 Cy3

tag: Genotype:	Mo17

tag: Sample name:	P3 Mo17 Cy5


title: S9_L

tag: Sample name:	P10 Mo17 Cy3

tag: Sample name:	P10 F1 Cy5


title: S12_L

tag: Sample name:	P5 B73 Cy3

tag: Sample name:	P5 Mo17 Cy5


title: S22_L

tag: Sample name:	P11 Mo17 Cy3

tag: Sample name:	P11 F1 Cy5


title: S13_L

tag: Tissue

tag: Dev stage

tag: Sample name:	P6 F1 Cy3

tag: Sample name:	P6 Mo17 Cy5


title: HPV 16 immortalized keratinocytes (VUMC_MCF29cl3_b2s70)

tag: HPV 16 immortalized keratinocytes

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


title: S25_L

tag: Genotype:	F1

tag: Sample name:	P12 F1 Cy3

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P12 Mo17 Cy5


title: S2_L

tag: Genotype:	B73

tag: Sample name:	P2 B73 Cy3

tag: Genotype:	Mo17

tag: Sample name:	P2 Mo17 Cy5


title: S17_L

tag: Sample name:	P7 F1 Cy3

tag: Sample name:	P7 Mo17 Cy5


title: S18_L

tag: Tissue

tag: Sample name:	P7 Mo17 Cy3

tag: Sample name:	P7 B73 Cy5


title: S10_L

tag: Dev stage

tag: Sample name:	P5 Mo17 Cy3

tag: Sample name:	P5 F1 Cy5


title: S16_L

tag: Sample name:	P7 B73 Cy3

tag: Genotype:	F1

tag: Sample name:	P7 F1 Cy5


title: S1_L

tag: Sample name

value: P2 F1 Cy3

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P2 B73 Cy5


title: S8_L

tag: Genotype:	B73

tag: Sample name:	P10 B73 Cy3

tag: Genotype:	Mo17

tag: Sample name:	P10 Mo17 Cy5


title: S14_L

tag: Tissue

tag: Sample name:	P6 Mo17 Cy3

tag: Sample name:	P6 B73 Cy5


title: S5_L

tag: Dev stage

tag: Sample name:	P3 B73 Cy3

tag: Sample name:	P3 F1 Cy5


title: S7_L

tag: Sample name:	P10 F1 Cy3

tag: Sample name:	P10 B73 Cy5


title: Vero cell_5 days_postinfection_11_Day5 control/Day5 pi.

status: Public on Jun 11 2008

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: No

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 50 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 2 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

organism:
Homo sapiens
Betapolyomavirus hominis

source_name: Control samples corresponding to 5 day

label_protocol: 3DNA Array 50 kit was used for fluorescence labeling on cDNA. Each total RNA (20μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column and was blocked by addictive 0.5μg of Cot1 human DNA.

growth_protocol: Vero cells, a line of African green monkey normal kidney epithelial cell (American Type Culture Collection, Manassas, Va.), were used throughout this study. Monolayer cultures of the cells were propagated in Eagle’s minimal essential medium (EMEM) (Mediatech Inc., Herndon, Va.), supplemented with 5% heat-inactivated fetal bovine serum (Mediatech Inc.) equilibrated with 5% CO2, in a humidified 37°C incubator. BK virus Gardner strain was kindly supplied by Dr. Walter Atwood (Brown University, Providence, RI) for use in infection experiments. Virus was processed and maintained as described previously(6). During infection procedure, Vero cells were grown at 37°C in T75 spinner flasks to a cell density of approximately 70% confluence prior to infection. Stocks of virus particles were appropriately diluted in EMEM culture medium supplemented with2% FBS/1% P/S in a volume sufficient to cover the cells. Infections were performed at a multiplicity of infection (MOI) of 5 PFU/cell at room temperature and virus was allowed to adhere to cells for one hour at 37°C, 5% CO2 with gentle rocking every 15 minutes to ensure that the inoculums were evenly distributed. After adsorption, complete media were then added and the infected cells were incubated at 37°C, 5% CO2 in a humidified incubator. At the indicated times post-infection (5, 10, 15, 19, and 25 dpi), the virus-containing culture medium was removed and the cells were washed twice gently with in phosphate buffered saline (PBS) directly in the flask. Remained PBS was taken away as far as possible and 2 ml of Trizol reagent (Invitrogen, Carlsbad, CA) were added into each flask. The infected cells were lysed entirely and harvested by pipetting up and down to lift the cells from the surface of flask. Finally, the cell lysates were transferred into 1.5-ml fresh microcentrifuge tubes on ice, and then frozen at -80°C until preparation of RNA. Mock-infected control cells were treated and harvested in the same manner as those infected, except that EMEM without virus was used during the infection.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 2.0 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: NO

tag: The Vero lineage was isolated from kidney epithelial cells extracted from African green monkey (Cercopithecus aethiops). The lineage was developed on 27 Mar 1962, by Yasumura and Kawakita at the Chiba University in Chiba, Japan.

source_name: Sample harvested at 5 day after BKV infection


title: S3_L

tag: Sample name:	P2 Mo17 Cy3

tag: Genotype:	F1

tag: Sample name:	P2 F1 Cy5


title: Vero cell_10 days and 19 days_postinfection_17_Day10 pi./Day19 pi.

description: No

source_name: Sample harvested at 10 day after BKV infection

source_name: Sample harvested at 19 day after BKV infection


title: Vero cell_10 days_postinfection_6_Day5 control/Day10 pi.

description: No

treatment_protocol: Sample harvested at 10 day after BKV infection


title: Vero cell_15 days_postinfection_3_Day15 pi./Day15 control

description: No

source_name: Sample harvested at 15 day after BKV infection

source_name: Control samples corresponding to 15 day


title: Vero cell_19 days_postinfection_8_Day15 control/Day19 pi.

description: No

treatment_protocol: Sample harvested at 19 day after BKV infection


title: Vero cell_15 days and 25 days_postinfection_18_Day25 pi./Day15 pi.

description: No

source_name: Sample harvested at 25 day after BKV infection

treatment_protocol: Sample harvested at 15 day after BKV infection


title: S4_L

tag: Sample name:	P3 Mo17 Cy3

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P3 B73 Cy5


title: Vero cell_5 days_postinfection_10_Day25 control/Day5 pi.

description: No

source_name: Control samples corresponding to 25 day

treatment_protocol: Sample harvested at 5 day after BKV infection


title: Vero cell_15 days_postinfection_20_Day15 pi./Day15 pi.

description: No

treatment_protocol: Sample harvested at 25 day after BKV infection


title: S11_L

tag: Sample name:	P5 F1 Cy3

tag: Genotype:	B73

tag: Sample name:	P5 B73 Cy5


title: Vero cell_25 days_postinfection_15_Day25 control/Day25 pi.

description: No


title: Vero cell_19 days_postinfection_14_Day19 control/Day19 pi.

description: No

source_name: Control samples corresponding to 19 day


title: Vero cell_5 days_postinfection_16_Day15 control/Day5 pi.

description: No


title: Vero cell_15 days_postinfection_13_Day15 control/Day15 pi.

description: No


title: Vero cell_25 days_postinfection_9_Day19 control/Day25 pi.

description: No


title: Vero cell_15 days_uninfection_19_Day15 control/Day15 control

description: No


title: Vero cell_15 days_postinfection_7_Day10 control/Day15 pi.

description: No

source_name: Control samples corresponding to 10 day


title: Vero cell_10 days_postinfection_2_Day10 pi./Day10 control

description: No


title: 80post vs. 80pre

status: Public on Jun 05 2008

city: St. Lucia

first: Milena

last: Gongora

state: QLD

address: bld 80, services rd

country: Australia

institute: Institute for Molecular Biosciences

description: Dye-swap. In the normalized data, they were reversed

hyb_protocol: hyb buffer: 50% formamide, 1X SSC, 0.1%SDS, hybridised in a dark, humidified chamber at 42 oC for 14 hours

scan_protocol: Data was collected using the Agilent 5mM DNA microarray scanner, and images extracted using Digital Genome Molecularware software

data_processing: To account for dye swap, the signal channel and control channel measurements for samples 60_3 and 80_3 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement.

source_name: Bre-80-post selection

label_protocol: aRNA was amplified using an Ambion Amino Allyl  Message Amp aRNA kit

growth_protocol: HMECS were cultured in only MCDB-170 medium (Gibco, Invitrogen Corporation, Carlsbad (CA)) containing gentamycin (ul/ml) at 37oC in 5% CO2

extract_protocol: TRIZOL reagent

treatment_protocol: 48hours post AZA treatment (3µM 5-Aza-2’-deoxycytidine (5-Aza-dC) (Sigma) for 24 hours)

tag: AGE

value: 36year old female

tag: breast tissue from reduction mammoplasty in patient Bre 80.

tag: Cells:Primary Human Mammary Epithelial Cell line Bre-80

tag: passage 25

tag: untreated

source_name: Bre-80-pre selection

tag: Cells

tag: passage 4


title: 80postAZA vs. 80post

source_name: Bre-80-AZA treatment

tag: 48hours post AZA treatment

value: Primary Human Mammary Epithelial Cell line Bre-80


title: Vero cell_10 days_postinfection_12_Day10 control/Day10 pi.

description: No

tag: The Vero lineage was isolated from kidney epithelial cells extracted from African green monkey (Cercopithecus aethiops). The lineage was developed on 27 Mar 1962, by Yasumura and Kawakita at the Chiba University in Chiba, Japan.


title: LXIDN CD34+

status: Public on Jun 03 2008

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430_2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 2μg of total RNA.

hyb_protocol: Affymetrix Human HG-U133A GeneChip arrays hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA).The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=100. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

label: biotin

source_name: CB CD34+ progenitors cells

label_protocol: One-cycle target labeling assays was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 2 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Human CD34+ cells were seeded (5-10 x 105 / ml) in IMDM (Euroclone) containing 30% human serum (Biowhittaker) and early acting human hematopoietic cytokines: 50 ng/ml stem cell factor (SCF) and Flt3-ligand (Flt3-l), 20 ng/ml thrombopoietin (TPO), interleukin-6 (IL-6) and interleukin-3 (IL-3) (R&D Systems, Minneapolis, MN).

extract_protocol: Total cellular RNA was extracted from 0.5x105 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. RNAs originating from 3 different experiments were pooled in order to obtain at least 2 μg per sample.

treatment_protocol: Transduction of human CB CD34+ progenitors was performed after 48 h pre-activation by two cycles of infection (12 h each) with viral supernatant in the presence of polybrene (8 µg/ml) on retronectin-coated plates (10 µg/cm2) followed by 48 h post-incubation in the already described liquid culture conditions. Transduced CD34+ cells were subsequently purified by an immunomagnetic procedure using mouse anti-human p75-NGFR MoAb and tiny FACS-compatible magnetic nanoparticles in a column-free magnetic system (EasySepTM “Do-It-Your Self” Selection Kit; Stem cells Technologies) following the manufacturer guidelines.

tag: CD34+ hematopoietic progenitors purified from cord blood (CB).

tag: Human CD34+ cells were purified from umbilical cord blood samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lymphoprep; Nycomed Pharma, Oslo, Norway) gradient separation, washed twice with PBS, and then CD34+ cells separated using magnetic cell sorting procedure (EasySep Human CD34+ positive selection kit, StemCell Techonologies Inc.; Vancouver, Canada). CD34+ cell purity assessed by flow cytometry were always >95%.


title: virulent Rickettsia rickettsii Sheila Smith rep 1

status: Public on Jun 04 2008

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from__virulent Rickettsia rickettsii Sheila Smith_rep 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rickettsia rickettsii

source_name: virulent rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monolayers of Vero cells in T25 tissue culture flasks were infected with R. rickettsii Iowa and R. rickettsii R strain at an MOI of 0.05 and grown for 3 days.

extract_protocol: To harvest RNA the media was removed and 1 ml of Trizol (Invitrogen) was added to each T25 for RNA extraction.  200 µl of chloroform was added to the Trizol samples and spun at 13,000 rpm for 15 min.  The aqueous phase (~750 µl) was removed and dried to ~200 µl and the RNA was purified using RNeasy 96 Kit (Qiagen) according to the manufactures instructions.

tag: Sheila Smith


title: NT CD34+


title: 60postAZA vs. 60post

source_name: Bre-60-AZA treatment

value: 26year old female

tag: breast tissue from reduction mammoplasty in patient Bre 60.

tag: Cells:Primary Human Mammary Epithelial Cell line Bre-60

tag: passage 7

source_name: Bre-60-post selection


title: virulent Rickettsia rickettsii Sheila Smith rep 2

description: Gene expression data from__virulent Rickettsia rickettsii Sheila Smith_rep 2

source_name: virulent rep 2


title: Vero cell_25 days_postinfection_5_Day25 pi./Day25 control

description: No


title: Vero cell_19 days_postinfection_4_Day19 pi./Day19 control

description: No


title: MOCK CD34+

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

growth_protocol: To achieve an optimal expansion and differentiation of the primary CD34+ hematopoietic stem/progenitor cells, a serum-free liquid culture was performed by seeding CD34+ cells in 12-well plates at a density of 1x105/ml (2 ml/well) in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO), containing 20% BIT (BIT serum substitute: Bovine serum albumin, Insulin and Transferrin, StemCell Techonologies Inc.), SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-6 (10 ng/ml) and TPO (10 ng/ml) (all from R&D Systems).

treatment_protocol: Nucleofection of CD34+ stem/progenitor cells was performed according to the optimized protocol provided by the manufacturer, with several modifications (Amaxa Biosystem, Cologne, Germany; www.amaxa.com). 24 hours prior to electroporation the primary CD34+ hematopoietic cells were seeded in 24-well plates at a density of 5x105/ml in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) cointaining 20% HS (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). CD34+ cells were subjected to three cycle of nucleofection every 24h. Briefly, for each electroporation 5x105 cells were gently resuspended in 100 µl of Human CD34+ Nucleofector SolutionTM (Amaxa Biosystem), mixed with 5 µg of a mixture of 4 siRNAs targeting CD34 mRNA (SMARTpool, Dharmacon, Lafayette, CO, USA) and pulsed with the program U-01. As a control, in a separate sample, a non-targeting siRNA (siCONTROL Non-Targeting Pool, Dharmacon) was used. Immediately after nucleofection cells were transferred into pre-warmed fresh medium in 24-well plates. Cells were analyzed 24-48 hours after third nucleofection for both viability and CD34 antigen expression.


title: Vero cell_5 days_postinfection_1_Day5 pi./Day5 control

description: No

source_name: Sample harvested at 5 day after BKV infection

source_name: Control samples corresponding to 5 day


title: 60post vs. 60pre

tag: passage 2

source_name: Bre-60-pre selection

value: Primary Human Mammary Epithelial Cell line Bre-60


title: 60post vs. 60post


title: 80post vs. 80post


title: SM/J

status: Public on May 01 2008

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: epididymal fat was taken from 2 25-week old males and pooled

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA

organism: Mus musculus

source_name: SM/J

label_protocol: Three micrograms of total RNA was processed to produce biotinylated cRNA targets using standard Affymetrix procedures

extract_protocol: Samples were taken from epididymal fat and frozen on dry ice.  Frozen tissues were individually pulverized.  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).  For each strain, RNA was pooled so that the final amount was 3 micrograms total RNA, with each mouse represented in equal proportions.  The number of mice pooled per strain is noted under the Sample Description section.

tag: SM/J


title: SPRET/EiJ

source_name: SPRET/EiJ

tag: SPRET/EiJ


title: P aeruginosa PAO1 WT UW LB biofilm 7 h 30C

status: Public on May 29 2008

city: College Station

first: Can

last: Attila

state: TX

address: 524 Jack E. Brown Bldg.

department: Chemical Eng

institute: Texas A&M University

description: RNA extracted from biofilm cells of P. aeruginosa wild type UW after 7 hours of growth in LB with glass wool

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: Channel 1

label_protocol: Affymetrix

extract_protocol: Qiegen RNeasy Mini Kit


title: NZW/LacJ

description: epididymal fat was taken from 3 25-week old males and pooled

source_name: NZW/LacJ

tag: NZW/LacJ


title: MSM/Ms

source_name: MSM/Ms

tag: MSM/Ms


title: avirulent Rickettsia rickettsii Iowa rep 3

description: Gene expression data from__avirulent Rickettsia rickettsii Iowa_rep 3

source_name: avirulent rep 3

tag: Iowa


title: virulent Rickettsia rickettsii Sheila Smith rep 3

description: Gene expression data from__virulent Rickettsia rickettsii Sheila Smith_rep 3

source_name: virulent rep 3


title: JF1/Ms


title: LCD34IDN CD34+


title: avirulent Rickettsia rickettsii Iowa rep 1

description: Gene expression data from__avirulent Rickettsia rickettsii Iowa_rep 1

source_name: avirulent rep 1


title: siRNA CD34+


title: avirulent Rickettsia rickettsii Iowa rep 2

description: Gene expression data from__avirulent Rickettsia rickettsii Iowa_rep 2

source_name: avirulent rep 2


title: SWR/J

source_name: SWR/J

tag: SWR/J


title: NegCTR siRNA CD34+

source_name: CB CD34+ progenitors cells


title: CZECHII/EiJ

source_name: CZECHII/EiJ

tag: CZECHII/EiJ


title: PA2663 UW LB Biofilm cells 7 h

description: RNA extracted from biofilm cells of P. aeruginosa PAO1/PA2663 mutant after 7 hours of growth in LB with glass wool

extract_protocol: Qiagen RNeasy Mini Kit


title: SEA/GnJ

source_name: SEA/GnJ

tag: SEA/GnJ


title: SJL/J

source_name: SJL/J

tag: SJL/J


title: WSB/EiJ

source_name: WSB/EiJ

tag: WSB/EiJ


title: CAST/EiJ

source_name: CAST/EiJ

tag: CAST/EiJ


title: RIIIS/J

source_name: RIIIS/J

tag: RIIIS/J


title: PERA/EiJ

description: epididymal fat was taken from 1 25-week old males and pooled

source_name: PERA/EiJ

tag: PERA/EiJ


title: NZB/BlNJ

source_name: NZB/BlNJ

tag: NZB/BlNJ


title: C57L/J


title: BTBR_T+_tf/J


title: PL/J

source_name: PL/J

tag: PL/J


title: NOD/LtJ

source_name: NOD/LtJ

tag: NOD/LtJ


title: MOLF/EiJ

source_name: MOLF/EiJ

tag: MOLF/EiJ


title: DBA/2J


title: FVB/NJ

source_name: FVB/NJ

tag: FVB/NJ


title: C57BL/6J


title: C3H/HeJ

description: epididymal fat was taken from 4 25-week old males and pooled


title: CBA/J

source_name: CBA/J

tag: CBA/J


title: WT_Doxorubicinvs.WT_4

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: The gene expression of the whole heart of Doxorubicin treated wildtype mice was compared with wildtype mice.

hyb_protocol: Targets were vacuum-centrifuged and resuspended in 50 μl DIG hybridisation buffer (Roche). Denatured targets (98°C, 2 min) were hybridised in a humidified chamber at 42°C overnight. The following day arrays were washed (2xSSC; 0,03% SDS for 10min, 2xSSC for 5min, 1xSSC for 5min, 0,2 x SSC for 2min) and dried in a centrifuge.

scan_protocol: Agilent Microarray scanner (G2565BA)

data_processing: Local background was subtracted and LOWESS normalisation was performed using Feature Extraction Software (version A 6.1.1).

source_name: wildtype mice

label_protocol: Labeling of the targets during reverse transcription was performed as described by Pat Brown (http://brownlab.stanford.edu/).

growth_protocol: Animals were kept in a SPF barrier under standardisized conditions with respect to temperature and humidity, and were housed on a 12h light/12h dark cycle in groups of 4-5 with free access to food and water. Animal housing, care, and applications of experimental procedures complied with the Guide for the Care and Use of Laboratory Animals of the Government of Berlin, Germany and are in accordance to the recommendations of the Society for Laboratory Animal Science (GV-SOLAS) and the Federation of European Laboratory Animal Science Associations (FELASA).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer`s instructions.

treatment_protocol: No treatment was applied.

tag: strain

tag: gender

value: male

tag: age

value: 10 months

tag: tissue

value: whole heart

source_name: wildtype mice treated with Doxorubicin

treatment_protocol: Wildtype mice were treated 3 times a week with 15mg/kg Doxorubicin.


title: WT_Doxorubicinvs.WT_1


title: BUB/BnJ

source_name: BUB/BnJ

tag: BUB/BnJ


title: BALB/cByJ

source_name: BALB/cByJ

tag: BALB/cByJ


title: AKR/J

source_name: AKR/J

tag: AKR/J


title: WT_Doxorubicinvs.WT_2


title: A/J

source_name: A/J

tag: A/J


title: ErbB2vs.WT_1

description: The gene expression of the whole heart of ErbB2 knockout mice was compared with wildtype mice.

source_name: ErbB2 knockout mice


title: ErbB2vs.WT_2


title: ErbB2vs.WT_3


title: ErbB2vs.WT_4


title: MLPvs.WT_2

description: The gene expression of the whole heart of MLP knockout mice was compared with wildtype mice.

source_name: MLP knockout mice


title: MLPvs.WT_3


title: Normal, Age 44 Normal adipose tissue obtained from the same patient as Tumor 32

type: genomic

city: Savannah

first: Jay

last: Johnson

state: GA

address: 4700 Waters Ave

institute: Memorial Health University Medical Center

data_processing: See "Pei, J., Kruger, W.D., and Testa, J.R. (2006). High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays. Cancer Genet Cytogenet 170, 65-68." Briefly, The intensity of probe signals following hybridization to the GeneChip was determined using Affymetrix GeneChip Operating Software v1.2. The Affymetrix Copy Number Analysis Tool v2.1 was used to generate copy number calls for each of 57,290 discreet SNP markers, using the default genomic smoothing window setting of 0.5 Mb. Copy number (CN) calls were generated using the Affymetrix Dynamic Model.

label: Biotin

molecule: genomic DNA

source_name: Normal Adipose Tissue

label_protocol: An overview of Affymetrix SNP labeling protocol is available at: www.affymetrix.com. Briefly, tumor genomic DNA was subjected to restriction digestion by XbaI and the resulting fragments were ligated to adaptor sequences and PCR amplified. This PCR product was then fragmented by treatment with DNaseI, denatured to generate single stranded product and end-labeled by terminal deoxynucleotidyl transferase.

extract_protocol: Genomic DNA was prepared from tumor samples by SDS lysis, proteinase K treatment and phenol extraction. DNA was checked for purity using a NanoDrop spectrophotometer and for excessive shearing by agarose gel electrophoresis.

tag: Normal, Age 44. Normal adipose tissue obtained from the same patient as Tumor 32.


title: Tumor 32, Grade 3, Age 44

hyb_protocol: See "Pei, J., Kruger, W.D., and Testa, J.R. (2006). High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays. Cancer Genet Cytogenet 170, 65-68."

source_name: Liposarcoma

tag: Tumor 32, Grade 3, Age 44, majority of the tumor lacks characteristics consistent with ALT- or telomerase-positivity.  Some cells may be telomerase-positive, however.


title: Tumor 26R2, Grade 2, Age 60, telomerase-positive  This tumor is a recurrence of Tumor 26R1

scan_protocol: See "Pei, J., Kruger, W.D., and Testa, J.R. (2006). High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays. Cancer Genet Cytogenet 170, 65-68."

tag: Tumor 26R2, Grade 2, Age 60, telomerase-positive.  This tumor is a recurrence of Tumor 26R1.


title: MLPvs.WT_4


title: Tumor 27R1, Grade 2, Age 69, telomerase-positive  This sample is a recurrence of Tumor 27

tag: Tumor 27R1, Grade 2, Age 69, telomerase-positive.  This sample is a recurrence of Tumor 27.


title: Tumor 27R2, Grade 2, Age 70, telomerase-positive  This sample is a recurrence of Tumor 27R1

tag: Tumor 27R2, Grade 2, Age 70, telomerase-positive.  This sample is a recurrence of Tumor 27R1.


title: Tumor 26R1, Grade 2, Age 60, neither ALT- or telomerase-positive  This tumor is a recurrence of Tumor 26

tag: Tumor 26R1, Grade 2, Age 60, neither ALT- or telomerase-positive.  This tumor is a recurrence of Tumor 26.


title: WT_Doxorubicinvs.WT_3


tag: Tumor 27, Grade 1, Age 69, telomerase-positive.


title: MLPvs.WT_1


tag: Tumor 28, Grade 1, Age 57, neither ALT- or telomerase-positive.


title: Plakoglobinvs.WT_4

description: The gene expression of the whole heart of plakoglobin knockout mice was compared with wildtype mice.

value: unknown

source_name: plakoglobin knockout mice


title: Plakoglobinvs.WT_2

description: The gene expression of the whole heart of plakoglobin knockout was compared with wildtype mice.

source_name: wildtype


tag: Tumor 26, Grade 1, Age 57, neither ALT- or telomerase-positive.


tag: Tumor 23, Grade 2, Age 52, telomerase-positive.


title: Tumor 30, Grade 3, Age 68, ALT-positive

tag: Tumor 30, Grade 3, Age 68, ALT-positive.


title: Plakoglobinvs.WT_3

tag: strain

tag: gender

tag: age


tag: Tumor 20, Grade 1, Age 74, telomerase-positive.


tag: Tumor 31, Grade 3, Age 78, neither ALT- or telomerase-positive.


title: ErbB4_Doxorubicinvs.WT_3

description: The gene expression of the whole heart of ErbB4 knockout mice treated with doxorubicin was compared with wildtype mice.

source_name: ErbB4 knockout mice treated with Doxorubicin

treatment_protocol: ErbB4 knockout mice were treated 3 times a week with 15mg/kg Doxorubicin.

tag: tissue


tag: Tumor 29, Grade 1, Age 59, neither ALT- or telomerase-positive.


title: Plakoglobinvs.WT_1


title: ErbB4vs.WT_4

description: The gene expression of the whole heart of ErbB4 knockout mice was compared with wiltdtype mice.

label_protocol: Labeling of the targets during reverse transcription was performed as decribed by Pat Brown (http://brownlab.stanford.edu/).

source_name: ErbB4 knockout mice


title: ErbB4_Doxorubicinvs.WT_2

growth_protocol: Growth protocol 	Animals were kept in a SPF barrier under standardisized conditions with respect to temperature and humidity, and were housed on a 12h light/12h dark cycle in groups of 4-5 with free access to food and water. Animal housing, care, and applications of experimental procedures complied with the Guide for the Care and Use of Laboratory Animals of the Government of Berlin, Germany and are in accordance to the recommendations of the Society for Laboratory Animal Science (GV-SOLAS) and the Federation of European Laboratory Animal Science Associations (FELASA).


tag: Tumor 11, Grade 1, Age 73, neither ALT- or telomerase-positive.


tag: Tumor 15, Grade 1, Age 64, telomerase-positive.


title: ErbB4_Doxorubicinvs.WT_4


title: ErbB4vs.WT_3

source_name: ErbB4 knockout Mice


tag: Tumor 10, Grade 1, Age 44, neither ALT- or telomerase-positive.


title: Cbf1 knockout expression

status: Public on Mar 18 2008

city: Cambridge

first: Joel

last: Moxley

state: MA

address: 77 Massachusettes Ave

institute: MIT

description: Cbf1 knockout expression

hyb_protocol: Whitehead LSP Automated Hyb

scan_protocol: Arrays were scanned at 10 micron resolution using either GenePix 4000A (Axon Instruments)

data_processing: normalized using qspline and modeled ratio error with VERA/SAM

label: Cy3 or Cy5

organism: Saccharomyces cerevisiae

label_protocol: Extracted mRNA was labeled with Cy3 or Cy5 by direct incorporation (Amersham CyScribe First-Strand cDNA Labeling Kit)

growth_protocol: Gene expression experiments were processed in parallel with at least two distinct biological samples from each strain (colonies of similar size picked from fresh YPD + G418 agar plates) grown to saturation in YNB overnight at 30°C. The overnight culture was diluted 1:100 in a flask of 100ml fresh YNB and grown in a shaking incubator at 30°C 180 rpm until the culture reached an OD600 of 0.8 – 1.0. Every effort was made to closely match the final optical density of each of the samples.

extract_protocol: Total RNA extraction with hot phenol

tag: cells grown in YNB media supplemented with 20 mg/L methionine

source_name: wt+met


title: Met32 knockout expression

description: Met32 knockout expression

tag: cells grown in YNB media

source_name: wt


title: ErbB4vs.WT_2

source_name: wildtype mice


title: Met31 knockout expression

description: Met31 knockout expression


title: ErbB4vs.WT_1


title: Met28 knockout expression

description: Met28 knockout expression

label: Cy5 or Cy3


tag: Tumor 9, Grade 1, Age 49, telomerase-positive with an intermediate ALT-phentype.


title: ErbB4_Doxorubicinvs.WT_1


title: Tumor 7, Grade 1, Age 72, ALT-positive

tag: Tumor 7, Grade 1, Age 72, ALT-positive.


title: dye-swap experiment between propagated callus and shoot 4

status: Public on Apr 01 2008

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: 10 days old shoot14' is control sample, and 'propagated_callus2' is target sample.

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 8.1.1.1
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Japonica Group

source_name: propagated callus2

label_protocol:
Kit: Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Linear Amplification kit standard protocol

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: callus induction medium
light condition: continuous light
temperature: 30 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

extract_protocol:
Separation technique: Trimming
Extraction source: Frozen
Kit: RNeasy Midi Kit
Manufacturer: QIAGEN
Manual: QIAGEN
Kit: OligotexTM-dt30 <Super> mRNA Purification kit (From Total RNA)
Manufacturer: TaKaRa
Manual: TaKaRa

tag: cultivar

value: Nipponbare

tag: Tissues

value: cultured callus

tag: stage

value: in-vitro culture stage

value: incubation for 21 days

source_name: 10 days old shoot14

growth_protocol:
growth: hydroponic culture
growth enviroment: growth chamber study
Growth substrates: 1/5000 diluted Hyponex (10-3-3) solution
light condition: 16hrs day length
temperature: 28 degreeC

tag: Tissue

value: shoot

value: LP.03 three leaves visible

value: 10 days after sowing


title: Tumor 5, Grade 1, Age 64, ALT-positive

tag: Tumor 5, Grade 1, Age 64, ALT-positive.


title: dye-swap experiment between propagated callus and shoot 3

tag: age


title: dye-swap experiment between redifferentiation callus and shoot 1

description: 10 days old shoot7' is control sample, and is same as sample of sample name shoot_self7. 'callus incubated on re-differential induced medium' is target sample, and is same as sample of sample name Redif_callus_self

source_name: 10 days old shoot7

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: redifferentiation medium
light condition: continuous light
temperature: 30 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

value: incubation for 35 days


title: Tumor 4, Grade 1, Age 73, ALT-positive

tag: Tumor 4, Grade 1, Age 73, ALT-positive.


title: dye-swap experiment between regenerated plant and shoot 2

description: 10 days old shoot7' is control sample, and is same as sample of sample name shoot_self7. 'regenerated plant from callus' is target sample, and is same as sample of sample name Reg_plant_self

source_name: regenerated plant from callus

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: hormone-free medium
light condition: 16hrs day length
temperature: 28 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

value: incubation for 52 days


title: dye-swap experiment between redifferentiation callus and shoot 2

source_name: callus incubated on re-differential induced medium


title: Tumor 3, Grade 1, Age 53, ALT-positive

tag: Tumor 3, Grade 1, Age 53, ALT-positive.


title: Tumor 2, Grade 1, Age 65, ALT-positive

tag: Tumor 2, Grade 1, Age 65, ALT-positive.


title: Tumor 1, Grade 1, Age 66, ALT-positive

data_processing: See "Pei, J., Kruger, W.D., and Testa, J.R. (2006). High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays. Cancer Genet Cytogenet 170, 65-68."  Briefly, The intensity of probe signals following hybridization to the GeneChip was determined using Affymetrix GeneChip Operating Software v1.2.  The Affymetrix Copy Number Analysis Tool v2.1 was used to generate copy number calls for each of 57,290 discreet SNP markers, using the default genomic smoothing window setting of 0.5 Mb.  Copy number (CN) calls were generated using the Affymetrix Dynamic Model.

label_protocol: An overview of Affymetrix SNP labeling protocol is available at: www.affymetrix.com.  Briefly, tumor genomic DNA was subjected to restriction digestion by XbaI and the resulting fragments were ligated to adaptor sequences and PCR amplified.  This PCR product was then fragmented by treatment with DNaseI, denatured to generate single stranded product and end-labeled by terminal deoxynucleotidyl transferase.

extract_protocol: Genomic DNA was prepared from tumor samples by SDS lysis, proteinase K treatment and phenol extraction.  DNA was checked for purity using a NanoDrop spectrophotometer and for excessive shearing by agarose gel electrophoresis.

tag: Tumor 1, Grade 1, Age 66, ALT-positive.


tag: Tumor 8, Grade 1, Age 76, neither ALT- nor telomerase-positive.


title: Healthy cervical tissue 2

status: Public on Mar 01 2008

first: Petra

last: Biewenga

address: Meibergdreef 9

department: Department Gynaecologic Oncology

institute: Academic Medical Centre

hyb_protocol: Hybidization was done according to the Agilent Hybridization procedure (protocol version 3.0)

scan_protocol: Scanned on a Agilent Technologies Scanner G2505A US14702369. Images were quantified using Agilent Feature Extraction Software (version A.7.5). For background correction local background and  spatial detrend was used.

data_processing: Default settings of the Agilent Feature Extraction pre-processing protocol were used to obtain raw intensity values from the scans. Exact protocol and parameter settings are described in the Agilent Feature Extraction Software User Manual 7.5 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=37629). Quality control of the Agilent Feature Extraction results was performed using methods available from Bioconductor packages (marray, limma, arrayQuality) in the statistical software package R. Intensities of negative and positive controls were inspected, as well as spatial effects, M/A plots, and signal-to-noise distributions.

source_name: RNA from healthy cervical tissue

label_protocol: RNA was amplified and converted to fluorescently labelled cDNA, with either cyanine 3 or cyanine 5. The Low RNA Input Fluorescent Linear Amplification Kit (Agilent) was used to synthesise labelled cRNA, for labelling we used 500 ng RNA.

growth_protocol: Tumour material was snapfrozen in liquid nitrogen at the pathology department after radical surgery

extract_protocol: Total RNA was isolated according to Trizol reagent protocol

tag: RNA from healthy cervical tissue

source_name: RNA pooled from all tumour tissue samples


title: Early stage cervical tumour with lymph node metastasis 23

source_name: RNA from early stage cervical cancer with lymph node metastasis

tag: Tumour stage

tag: RNA pooled from all tumour tissue samples


title: Early stage cervical tumour with lymph node metastasis 15, technical replicate

description:
P15.tr
technical replicate

value: IIA


title: Early stage cervical tumour with lymph node metastasis 21


title: Healthy cervical tissue 4


title: Healthy cervical tissue 1


title: Healthy cervical tissue 7


title: Healthy cervical tissue 3


title: Early stage cervical tumour without lymph node metastasis 23

source_name: RNA from early stage cervical cancer without lymph node metastasis


title: Early stage cervical tumour with lymph node metastasis 14, technical replicate

description:
P14.tr
technical replicate


title: Early stage cervical tumour with lymph node metastasis 14


title: Early stage cervical tumour with lymph node metastasis 15


title: Early stage cervical tumour without lymph node metastasis 27


title: Early stage cervical tumour with lymph node metastasis 10


title: Early stage cervical tumour with lymph node metastasis 7, technical replicate

description:
P7.tr
technical replicate


title: Early stage cervical tumour with lymph node metastasis 17


title: Early stage cervical tumour with lymph node metastasis 4


title: Early stage cervical tumour with lymph node metastasis 1


title: Early stage cervical tumour with lymph node metastasis 3


title: Early stage cervical tumour without lymph node metastasis 21


title: Early stage cervical tumour without lymph node metastasis 16, technical replicate

description:
N16.tr
technical replicate


title: Early stage cervical tumour without lymph node metastasis 26


title: Early stage cervical tumour with lymph node metastasis 6


title: Early stage cervical tumour with lymph node metastasis 8


title: Early stage cervical tumour with lymph node metastasis 24


title: Early stage cervical tumour with lymph node metastasis 19


title: Early stage cervical tumour without lymph node metastasis 22


title: Early stage cervical tumour with lymph node metastasis 13


title: Early stage cervical tumour without lymph node metastasis 20


title: Early stage cervical tumour with lymph node metastasis 7


title: PAO1-psrA::Tn LB replicate3

status: Public on Feb 14 2008

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

description: Samples processed at UCI DNA Microarray Facility (Irvine, CA)

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: Signal values determined using MAS5

source_name: PAO1-psrA::Tn LB replicate3

label_protocol: As per Affymetrix protocol for terminal labelling (used EnzoArray)

growth_protocol: Cells were grown in LB media and harvested at mid-log phase.

extract_protocol: Pseudomonas aeruginosa total RNA was isolated using Qiagen RNeasy mini kit, with an on-column DNaseI treatment.

tag: Pseudomonas aeruginosa total RNA was isolated from PAO1-psrA::Tn grown in LB


title: Early stage cervical tumour with lymph node metastasis 12


title: Early stage cervical tumour without lymph node metastasis 18


title: Early stage cervical tumour without lymph node metastasis 11


title: Early stage cervical tumour without lymph node metastasis 14


title: Early stage cervical tumour without lymph node metastasis 17


title: Early stage cervical tumour without lymph node metastasis 19


title: PAO1-psrA::Tn LB replicate1

source_name: PAO1-psrA::Tn LB replicate1

growth_protocol: Cells were grown in LB and harvested at mid-log phase.


title: PAO1-psrA::Tn LB replicate2

source_name: PAO1-psrA::Tn LB replicate2


title: PAO1 LB replicate1

description: Sample processed at UCI DNA Microarray Facility (Irvine, CA)

source_name: PAO1 LB replicate1

tag: Pseudomonas aeruginosa total RNA was isolated from PAO1 grown in LB


title: Early stage cervical tumour without lymph node metastasis 15


title: Early stage cervical tumour without lymph node metastasis 3


title: Early stage cervical tumour without lymph node metastasis 6


title: Early stage cervical tumour without lymph node metastasis 10


title: Early stage cervical tumour without lymph node metastasis 6, technical replicate

description:
N6.tr
Technical replicate of tumor N6


title: Early stage cervical tumour without lymph node metastasis 8


title: Early stage cervical tumour without lymph node metastasis 16


title: AA116

status: Public on Jan 01 2008

city: Minneapolis

first: Jeff

last: Lande

state: MN

address: 420 Washington Avenue SE

department: Medicine

institute: University of Minnesota

description: Bronchoalveolar lavage fluid from lung tx recipient with AB score = 0 (No rejection)

data_processing: Bioconductor - RMA - affy version 1.10.0

source_name: bronchoalveolar lavage cells (No rejection)

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: TRIzol w/ Qiagen RNeasy cleanup

tag: Male; Months since transplant=4; %PMN=1; %Lym=5


title: AA105

description: Bronchoalveolar lavage fluid from lung tx recipient with AB score = 3 (Rejection)

source_name: bronchoalveolar lavage cells (Rejection)

tag: Male; Months since transplant=5; %PMN=6; %Lym=6


title: PAO1 LB replicate2

source_name: PAO1 LB replicate2


title: AA104

tag: Male; Months since transplant=13; %PMN=0; %Lym=12


title: Early stage cervical tumour without lymph node metastasis 1


title: Early stage cervical tumour without lymph node metastasis 2


title: AA114

description: Bronchoalveolar lavage fluid from lung tx recipient with AB score = 1 (No rejection)

tag: Male; Months since transplant=3; %PMN=0; %Lym=0


title: AA98


title: AA115

tag: Male; Months since transplant=1; %PMN=14; %Lym=3


title: AA118

tag: Male; Months since transplant=1; %PMN=4; %Lym=5


title: AA97

tag: Female; Months since transplant=7; %PMN=1; %Lym=1


title: AA88

tag: Male; Months since transplant=9; %PMN=4; %Lym=18


title: AA85

description: Bronchoalveolar lavage fluid from lung tx recipient with AB score = 2 (Rejection)

tag: Female; Months since transplant=5; %PMN=0; %Lym=0


title: AA112

tag: Female; Months since transplant=20; %PMN=0; %Lym=0


title: AA113

tag: Male; Months since transplant=19; %PMN=1; %Lym=20


title: AA106

tag: Male; Months since transplant=1; %PMN=3; %Lym=1


title: AA99

tag: Male; Months since transplant=3; %PMN=1; %Lym=0


title: AA103

tag: Female; Months since transplant=5; %PMN=1; %Lym=3


title: AA78

tag: Female; Months since transplant=4; %PMN=0; %Lym=8


title: AA31

tag: Female; Months since transplant=7; %PMN=0; %Lym=7


title: AA100

tag: Female; Months since transplant=1; %PMN=1; %Lym=2


title: AA102

tag: Male; Months since transplant=8; %PMN=8; %Lym=1


title: AA96

tag: Male; Months since transplant=2; %PMN=0; %Lym=0


title: AA74

tag: Female; Months since transplant=2; %PMN=13; %Lym=5


title: AA72

tag: Male; Months since transplant=12; %PMN=2; %Lym=12


title: AA22

tag: Male; Months since transplant=6; %PMN=0; %Lym=8


title: soleus_short term heat acclimated rats (2dac)

status: Public on Dec 31 2007

city: Jerusalem

first: Michal

last: Horowitz

country: Israel

institute: The hebrew University

description: Gene expression data from soleus muscle following heat acclimation ( 34°C,2days)

hyb_protocol: The membranes were prehybridized for 1 h at 68°C in a hybridization solution (Clontech) containing 0.1 mg/ml sheared salmon testes DNA (Sigma) to block nonspecific binding. Synthesized radio labeled cDNA probe was applied to each membrane and hybridized overnight at 68°C. Cot-1 DNA (Clontech) (1 ug/ml) was added to block nonspecific binding.

scan_protocol: For analysis, the membranes were exposed for 15 and 24 h to a phosphor screen and detected using a Bio-imaging Analyzer BAS2000 (Fuji Photo Film Co. Ltd Japan.

data_processing: We used Atlas Image 2.01 software (Clontech) to grid the phosphor image, to record the pixel density of each spot, and to perform background subtraction. The background-subtracted data were then further analyzed.

organism: Rattus norvegicus

source_name: soleus

label_protocol: Standard Clontech protocol was used

extract_protocol: Total RNA was prepared from individual tissue samples using Tri-Reagent isolation protocol. Three pools (6 animals) were prepared for each experimental group.

tag: Sabra strain, males, 3 mo old, soleus


title: AA25

tag: Male; Months since transplant=6; %PMN=6; %Lym=0


title: AA79

tag: Male; Months since transplant=6; %PMN=1; %Lym=1


title: heart_control untreated rats

description: Gene expression data from left ventricle of rat heart

hyb_protocol: The membranes were prehybridized for 1 h at 68C in a hybridization solution (Clontech) containing 0.1 mg/ml sheared salmon testes DNA (Sigma) to block nonspecific binding. Synthesized radio labeled cDNA probe was applied to each membrane and hybridized overnight at 68°C. Cot-1 DNA (Clontech) (1 ug/ml) was added to block nonspecific binding.

source_name: heart

tag: Sabra strain, males, 3 mo old, heart


title: AA86

tag: Male; Months since transplant=7; %PMN=2; %Lym=4


title: heart_long-term heat acclimated rats (Acc)

description: Gene expression data from heart muscle following heat acclimation( (34°C,1mo)


title: AA77

tag: Male; Months since transplant=7; %PMN=3; %Lym=9


title: AA73


title: AA75

tag: Male; Months since transplant=6; %PMN=10; %Lym=1


title: soleus_long-term heat acclimated rats (Acc)

description: Gene expression data from soleus muscle following heat acclimation( (34°C,1mo)


title: heart_rats exposed to short-term heat acclimation and exercise training (3dexac)

description: Gene expression data from heart muscle following both exercise training ( treadmill , 24°C,3 days) and heat acclimation ( 34°C,3days)


title: soleus_rats exposed to short-term heat acclimation and exercise training (3dexac)

description: Gene expression data from soleus muscle following both exercise training ( treadmill , 24°C,3 days) and heat acclimation ( 34°C,3days)


title: soleus_rats exposed to long-term heat acclimation and exercise training (ExAc)

description: Gene expression data from soleus muscle following both exercise training ( treadmill , 24°C,1mo) and heat acclimation ( 34°C,1mo)


title: heart_long-term aerobic exercised trained rats (Ex)

description: Gene expression data from left ventricle of aerobic exrcise  trained (treadmill) (24°C,1mo)rat heart


title: AA59

tag: Female; Months since transplant=8; %PMN=0; %Lym=1


title: heart_short-term aerobic exercised trained rats (3dex)

description: Gene expression data from left ventricle of short exercise training (24°C,3days)rat heart


title: soleus_control untreated rats

description: Gene expression data from soleus


title: soleus_short term aerobic exercised trained rats (3dex)

description: Gene expression data from soleus muscle following short term of exercise training ( treadmill , 24°C,3days)


title: heart_rats exposed to long-term heat acclimation and exercise training (ExAc)

description: Gene expression data from heart muscle following both exercise training ( treadmill , 24°C,1mo) and heat acclimation ( 34°C,1mo)


title: soleus_long-term aerobic exercised trained rats (Ex)

description: Gene expression data from soleus muscle following exercise training ( treadmill , 24°C,1mo)


title: AA76

tag: Female; Months since transplant=4; %PMN=NA; %Lym=NA


title: heart_short-term heat acclimated rats (2dac)

description: Gene expression data from left ventricle of short heat acclimated (34°C,2days)rat heart


title: AA30

description: Bronchoalveolar lavage fluid from lung tx recipient with AB score = 0 (No rejection)

tag: Male; Months since transplant=10; %PMN=0; %Lym=0


title: 10mM LiCl treated N2 Replicate 6

status: Public on Dec 01 2007

city: Novato

first: Gawain

last: McColl

address: 8001 Redwood Blvd

institute: Buck Institute for Age Research

description: Biological replicate 6 of 6. Wildtype(N2) 10mM LiCl treated.

hyb_protocol: Using a Lucidea Slide Pro machine, the labeled aRNA was hybridized to a c.elegan oligo array, purchased from Washington University. The arrays were treated prior to shipment, so after the Lucidea performed a standard chamber wash, the array was loaded (array side-up) into the chamber, which was then locked into place. The control and experimental aRNA samples (Cy3 and Cy5) were combined and brought up to 92ul's with nuc-free water. Then an equal amount of hybridization buffer consisting of Genisphere’s 2X Formamide hybe buffer (C600V600S25) and 50% Dextran sulfate (final concentration, 1X Hybridization buffer and 2.5% Dextran Sulfate) were added to the sample along with LNA blocker (CW3920) from Genisphere. This mixture was heated and using a syringe injected into the Lucidea slide chamber portal. The solution was circulated over night at 42 degrees Celsius at a 30 minute cycle 10ul/second. Then the Lucidea washed the array using 4 washes in succession (2XSSC + 0.1% SDS, 2XSSC, 0.2XSSC and isopropanol) and then dried the array with air.

scan_protocol: Each array was scanned at 10um, using a Scan Array Express scanner. Using the control spots on the array, the two channels, Cy3 and Cy5 were equilibrated during a pre-scan, and brought within an equivalent range (equal amounts of Spot Report aRNA were spiked into both the Cy3 and Cy5 samples prior to labeling). Once the PMT and POW settings were adjusted, the array was scanned. First scanning Cy5 then Cy3.

data_processing: Each array was quantitated using Axon's GenePix 5.0 software and the provided gal file from Washington University. Both channels were loaded, inspected for defects and flagged accordingly. Then GenePix generated a gpr file to be used for downstream analysis.

organism: Caenorhabditis elegans

source_name: Amplified total RNA from 10mM LiCl treated worms labeled with Cyanine-5 (red).

label_protocol: 5ug's of aRNA, spiked with control aRNA (1-10 Spot Report Spikes), was dried with a speed vacuum in a 1.5ml eppendorf tube. Cy3/Cy5 CyDye Post Labeling Reactive Dyes from Amersham were re-suspended in DMSO (1 dye: 1 sample). The dried aRNA was re-suspended in coupling buffer, provided with the Ambion kit and mixed with the re-suspended dye. Controls were labeled with Cy3 and experimentals were labeled with Cy5. After the dyes coupled at room temperature they were purified using Ambion's provided columns and wash protocol. After elution, the labeled aRNA was fragmented using Ambion's Fragmentation kit (8740).

growth_protocol: cultured from egg at 20oC prior to treatment.  Shifted to 25oC for treatment for 48hr

extract_protocol: Total RNA was extracted from pellets of 50 worms (each sample consisted of 50 picked worms stored at -80 in an eppendorf tube until extraction) using Stratagene's Absolute RNA Microprep kit (400805). Using the Microprep kit components and columns, the worm pellets were extracted using a BME and lysis buffer solution and washed with a column using salt and ethanol wash buffers (provided with the kit). RNA was then Dnased using the kit components and then washed with a salt and ethanol buffer and eluted in nuclease-free water. Sample concentration was assessed using a Nanodrop.The entire total RNA sample was then amplified using Ambion's Amino Allyl Message Amp II kit (AM1795 and AM1796). Following the protocol, the total RNA was amplified one round. The concentration was then assessed with a Nanodrop and the quality of the aRNA was verified using Agilent's Bioanalyzer.

treatment_protocol: NGM + 10mM LiCl 25oC 48h

tag: Wildtype (N2)

tag: Sex

value: hermaphrodite

source_name: Total RNA from pooled mixed stage wildtype (N2) C. elegans, labeled with Cyanine-3 (green).

tag: Mixed stage


title: Liver from High Growth Rate Family Follow GH Treatment 3

status: Public on Dec 25 2007

city: Kearneysville

first: Scott

middle: A

last: Gahr

state: WV

address: 11861 Leetown Rd.

institute: NCCCWA/ARS/USDA

description: The images generated by the ScanArray Microarray Scanner (Perkin-Elmer, Inc., Waltham, MA) were processed and spots were quantitated using the ScanArray Express software (Perkin-Elmer, Inc., Waltham, MA). Data was collected using the adaptive circle method with background subtraction. The analysis was set to flag all spot with a signal of less than 1000 and signal to noise ratio of less than 3.

hyb_protocol: Microarray slides were prepared for hybridization by washing twice in 0.2% SDS for 5 minutes each, then rinsing in nanopure water for 5 minutes and finally rinsing in warmed nanopure water for 3 minutes. Slides were dried by centrifugation and placed at 60°C in the humidified InSlide OutTM Hybridization oven (Boekel Scientific Inc., Feasterville, PA). For each slide, 15 pmol of each dye was combined, concentrated with the Microcon YM-30 Concentrators (Millipore Corp, Billerica, MA) and mixed with 75 microliter of SlidHyb #2 (Ambion, Inc., Austin, TX) fir hybridization The combined sample in the hybridization buffer was heated to 95°C for 10 minute and the warmed mixture was pipette under a LifterSlipTM Cover Slip (Erie Scientific Company, Portsmouth, NH) on top of the slide. The slides were then hybridized at 50°C for 16 to 18 hrs in the InSlide Out Hybridization Oven (Boekel Scientific Inc., Feasterville, PA). Slides were washed on an orbital shaker for 5 minutes each in 2xSSC + 0.5% SDS, then 0.5X SSC and finally 0.05X SSC all at room temperature.

scan_protocol: All slides were scanned using a ScanArray Express Miroarray Scanner (Perkin-Elmer, Waltham, MA). All slides were scanned at 5 micron resolution with the PMT gain adjusted for ~1% of the spots saturated in each channel.

data_processing: The raw data intensities collected from two-channel arrays were pre-processed using scripts written in R language. These scripts included functions from the statistical packages marray, arrayQuality and limma from the Bioconductor project. The scripts for data processing are available upon request (roger.vallejo@ars.usda.gov).

label: Alexa Fluor 647

organism: Oncorhynchus mykiss

source_name: Liver Collected for ~200 g Trout Following Posilac Treatment

label_protocol: Complementary DNA containing amino-modified bases was synthesized form 20 micrograms of total RNA using Invitrogen’s Superscript Indirect cDNA labeling system (Invitrogen, Corp., Carlsbad, CA) and then labeled with the Alexa Fluor 555 or 647 dyes (Invitrogen, Corp., Carlsbad, CA) following the manufacturer’s protocol with minor modifications.

growth_protocol: Following injection, the tail fin was notched to allow identification during tissue collection. After the injection, the fish were returned to their tank for three days. Throughout the experiment all fish were fed at 2% BW with commercial trout food (55% protein and 15% fat, Zeilger Bros. Inc., Gardner PA).

extract_protocol: Total RNA was isolated from the muscle pools following the TRI-Reagent (Sigma-Aldrich Corp., St. Louis, MO) modification of the guanidine isothiocyanate/phenol-chloroform method (Chomczynski and Sacchi, 1987).

treatment_protocol: Fish were given a two week acclimation period to the new tanks prior to the initiation of the treatments. Fish from each family were randomly selected to receive one of three treatments: slow release GH injection (120 mg/kg BW, n=4 per family), vehicle injection (n=4 per family) or untouched controls (n=2 per family). For this study, PosilacTM slow release rbST was kindly provided by Dr. Gregg Bogosian (Monsanto Co., Creve Coeur, MO). For the injection, fish were anesthetized by submersion in 75 mg/L Tricaine Methane Sulfonate (Western Chemical, Ferndale WA). The fish were injected interpertionally just anterior to the pelvic fins using a tiburcliun syringe fixed with an 18 gauge needle.

tag: Single Rainbow Trout Liver; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment

label: Alexa Fluor 555

source_name: Liver from High Growth Rate Family Follow Vehicle Treatment 3

tag: Single Rainbow Trout Liver; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment


title: Liver from High Growth Rate Family Follow GH Treatment 2

source_name: Liver Collected for ~200 g Trout Following Posilac Treatment 2

tag: Single Rainbow Trout Liver; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Growth Hormone Treatment Replicate 2

source_name: Liver Collected for ~200 g Trout Following Vehicle Treatment 2

label_protocol: Complementary DNA containing amino-modified bases was synthesized form 20 micrograms of total RNA using Invitrogen’s Superscript Indirect cDNA labeling system (Invitrogen, Corp., Carlsbad, CA) and then labeled with the Alexa Fluor 555 or 647 dyes (Invitrogen, Corp., Carlsbad, CA) following the manufacturer’s protocol with minor modifications

tag: Single Rainbow Trout Liver; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2


title: 10mM LiCl treated N2 Replicate 4

description: Biological replicate 4 of 6. Wildtype(N2) 10mM LiCl treated.


title: 10mM LiCl treated N2 Replicate 1

description: Biological replicate 1 of 6. Wildtype(N2) 10mM LiCl treated.


title: Control N2 Replicate 6

description: Biological replicate 6 of 6. Wildtype(N2) untreated control.

source_name: Amplified total RNA from untreated worms labeled with Cyanine-5 (red).

treatment_protocol: NGM 25oC 48h


title: Liver from Low Growth Rate Family Follow GH Treatment 1

source_name: Liver Collected for ~150 g Trout Following Posilac Treatment 1

tag: Single Rainbow Trout Liver; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone Treatment

source_name: Liver Collected for ~150 g Trout Following Vehicle Treatment 1

tag: Single Rainbow Trout Liver; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment


title: Control N2 Replicate 4

description: Biological replicate 4 of 6. Wildtype(N2) untreated control.


title: 10mM LiCl treated N2 Replicate 5

description: Biological replicate 5 of 6. Wildtype(N2) 10mM LiCl treated.


title: Liver from Low Growth Rate Family Follow GH Treatment 4

source_name: Liver Collected for ~150 g Trout Following Vehicle Treatment 4

tag: Single Rainbow Trout Liver; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2

source_name: Liver Collected for ~150 g Trout Following Posilac Treatment 4

tag: Single Rainbow Trout Liver; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone treatment Replicate


title: Liver from High Growth Rate Family Follow GH Treatment 4

source_name: Liver Collected for ~200 g Trout Following Vehicle Treatment 4

tag: Single Rainbow Trout Liver; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2

source_name: Liver Collected for ~200 g Trout Following Posilac Treatment 4

tag: Single Rainbow Trout Liver; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment Replicate 2


title: Control N2 Replicate 1

description: Biological replicate 1 of 6. Wildtype(N2) untreated control.


title: Liver from Low Growth Rate Family Follow GH Treatment 2

source_name: Collected for ~150 g Trout Following Posilac Treatment 2

tag: Single Rainbow Trout Liver; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone treatment Replicate 2

source_name: Liver Collected for ~150 g Trout Following Vehicle Treatment 2

tag: Single Rainbow Trout Liver; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2


title: Liver from High Growth Rate Family Follow GH Treatment 1

source_name: Liver Collected for ~200 g Trout Following Posilac Treatment 1

tag: Single Rainbow Trout Liver; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Growth Hormone Treatment

source_name: Liver Collected for ~200 g Trout Following Vehicle Treatment 1

tag: Single Rainbow Trout Liver; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment


title: 10mM LiCl treated N2 Replicate 3

description: Biological replicate 3 of 6. Wildtype(N2) 10mM LiCl treated.

source_name: Amplified total RNA from 10mM LiCl treated worms labeled with Cyanine-5 (red).

tag: Wildtype (N2)


title: Muscle from Low Growth Rate Family Follow GH Treatment 2

source_name: Muscle Collected for ~150 g Trout Following Posilac Treatment 2

tag: Single Rainbow Trout White Muscle Sample; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone treatment Replicate 2

source_name: Muscle Collected for ~150 g Trout Following Vehicle Treatment 2

tag: Single Rainbow Trout White Muscle Sample; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2


title: Muscle from High Growth Rate Family Follow GH Treatment 1

source_name: Muscle Collected for ~200 g Trout Following Vehicle Treatment 1

tag: Single Rainbow Trout White Muscle Sample ; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment

source_name: Muscle Collected for ~200 g Trout Following Posilac Treatment 1

tag: Single Rainbow Trout White Muscle Sample; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment


title: Muscle from Low Growth Rate Family Follow GH Treatment 4

source_name: Muscle Collected for ~150 g Trout Following Posilac Treatment 4

tag: Single Rainbow Trout White Muscle Sample; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Growth Horrmone treatment Replicate 2

source_name: Muscle Collected for ~150 g Trout Following Vehicle Treatment 4

tag: Single Rainbow Trout White Muscle Sample; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2


title: 10mM LiCl treated N2 Replicate 2

description: Biological replicate 2 of 6. Wildtype(N2) 10mM LiCl treated.

tag: Sex

source_name: Total RNA from pooled mixed stage wildtype (N2) C. elegans, labeled with Cyanine-3 (green).

tag: Mixed stage


title: Control N2 Replicate 2

description: Biological replicate 2 of 6. Wildtype(N2) untreated control.

source_name: Amplified total RNA from untreated worms labeled with Cyanine-5 (red).


title: Muscle from High Growth Rate Family Follow GH Treatment 3

source_name: Muscle Collected for ~200 g Trout Following Posilac Treatment 3

tag: Single Rainbow Trout White Muscle Sample; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment

source_name: Muscle Collected for ~200 g Trout Following Vehicle Treatment 3

tag: Single Rainbow Trout White Muscle Sample; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment


title: Liver from Low Growth Rate Family Follow GH Treatment 3

source_name: Liver Collected for ~150 g Trout Following Vehicle Treatment 3

tag: Single Rainbow Trout Liver; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment

source_name: Liver Collected for ~150 g Trout Following Posilac Treatment 3

tag: Single Rainbow Trout Liver; From Lot 63 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment


title: Muscle from High Growth Rate Family Follow GH Treatment 4

source_name: Muscle Collected for ~200 g Trout Following Vehicle Treatment 4

tag: Single Rainbow Trout White Muscle Sample; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment Replicate 2

source_name: Muscle Collected for ~200 g Trout Following Posilac Treatment 4

tag: Single Rainbow Trout White Muscle Sample; From Lot 28 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment Replicate 2


title: Muscle from Low Growth Rate Family Follow GH Treatment 1

source_name: Muscle Collected for ~150 g Trout Following Vehicle Treatment 1

tag: Single Rainbow Trout White Muscle Sample; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment

source_name: Muscle Collected for ~150 g Trout Following Posilac Treatment

tag: Single Rainbow Trout White Muscle Sample; From Lot 67 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone treatment


title: Muscle from High Growth Rate Family Follow GH Treatment 2

source_name: Muscle Collected for ~200 g Trout Following Posilac Treatment 2

tag: Single Rainbow Trout White Muscle Sample; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Growth Hormone treatment, Replicate 2

source_name: Muscle Collected for ~200 g Trout Following Vehicle Treatment 2

tag: Single Rainbow Trout White Muscle Sample; From Lot 155 Selected for High Growth Rate, Collected following 3 Day Vehicle treatment, Replicate 2


title: Diffuse large B-cell lymphoma  VUMC_L93_b32_s72

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

description: protocols available via the VUMC MACF website

hyb_protocol: Hybridization protocol available via the VUMC MACF website Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Using ImaGene as described in Carvalho et al (2004) J.Clin.Path., vol. 57, 644-646. Normalization was done to the mode value of the log2ratio's.

source_name: Lymph node

label_protocol:
DNA labeling protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol:
DNA isolation protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: Diffuse large B-cell lymphoma

source_name: Male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Pooled DNA from the blood of 10 normal individuals

tag: Gender


title: Control N2 Replicate 3

description: Biological replicate 3 of 6. Wildtype(N2) untreated control.

tag: Wildtype (N2)


title: Control N2 Replicate 5

description: Biological replicate 5 of 6. Wildtype(N2) untreated control.


title: Muscle from Low Growth Rate Family Follow GH Treatment 3

source_name: Muscle Collected for ~150 g Trout Following Vehicle Treatment 3

tag: Single Rainbow Trout White Muscle Sample; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Vehicle treatment

source_name: Muscle Collected for ~150 g Trout Following Posilac Treatment 3

tag: Single Rainbow Trout White Muscle Sample; From Lot 63 Selected for Low Growth Rate, Collected following 3 Day Growth Hormone treatment


title: Diffuse large B-cell lymphoma VUMC_L59_b32_s46

description: protocols available via VUMC MACF website

hyb_protocol: Hybridization protocol available via VUMC MACF website Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

source_name: lymph node

label_protocol:
DNA labeling protocol available via VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol:
DNA isolation protocol available via VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

value: female


title: Diffuse large B-cell lymphoma  VUMC_L77_b32_s55

source_name: Female reference DNA


title: Diffuse large B-cell lymphoma VUMC_L82_b32_s58


title: Diffuse large B-cell lymphoma  VUMC_L79_b32_s56


title: Diffuse large B-cell lymphoma VUMC_L86_b32_s62


title: Diffuse large B-cell lymphoma VUMC_L56_b32_s43


title: Diffuse large B-cell lymphoma  VUMC_L60_b32_s47


title: Diffuse large B-cell lymphoma VUMC_L57_b32_s44


title: Diffuse large B-cell lymphoma  VUMC_L73_b32_s51


title: Diffuse large B-cell lymphoma  VUMC_L74_b32_s52


title: Diffuse large B-cell lymphoma  VUMC_L70_b32_s48


title: Diffuse large B-cell lymphoma VUMC_L58_b32_s45


title: Diffuse large B-cell lymphoma  VUMC_L71_b32_s49


title: Diffuse large B-cell lymphoma VUMC_L46_b32_s35

tag: Burkitt lymphoma


title: Diffuse large B-cell lymphoma VUMC_L50_b32_s37


title: Diffuse large B-cell lymphoma  VUMC_L41_b32_s26


title: Diffuse large B-cell lymphoma  VUMC_L52_b32_s70


title: Diffuse large B-cell lymphoma VUMC_L44_b32_s31


title: Diffuse large B-cell lymphoma  VUMC_L54_b32_s41


title: Diffuse large B-cell lymphoma  VUMC_L51_b32_s38


title: Diffuse large B-cell lymphoma VUMC_L30_b32_s25


title: Diffuse large B-cell lymphoma  VUMC_L42_b32_s27


title: Diffuse large B-cell lymphoma  VUMC_L88_b32_s64

source_name: lymphnode


title: Diffuse large B-cell lymphoma VUMC_L26_b32_s22


title: Diffuse large B-cell lymphoma VUMC_L25_b32_s29


title: Diffuse large B-cell lymphoma  VUMC_L43_b32_s30


title: Diffuse large B-cell lymphoma VUMC_L24_b32_s28


title: Diffuse large B-cell lymphoma  VUMC_L48_b32_s69


title: Diffuse large B-cell lymphoma VUMC_L29_b32_s24


title: Diffuse large B-cell lymphoma VUMC_L23_b32_s21


title: Diffuse large B-cell lymphoma VUMC_L21_b32_s20


title: Diffuse large B-cell lymphoma VUMC_L17_b32_s16


title: Diffuse large B-cell lymphoma VUMC_L01_b32_s75

source_name: female reference DNA


title: Diffuse large B-cell lymphoma VUMC_L07_b32_s81


title: Diffuse large B-cell lymphoma VUMC_L18_b32_s17


title: Diffuse large B-cell lymphoma VUMC_L20_b32_s19


title: Diffuse large B-cell lymphoma VUMC_L02_b32_s76


title: Diffuse large B-cell lymphoma VUMC_L10_b32_s83


title: slide 7 cy5 untreated cy3 Nur77

status: Public on Nov 04 2007

first: Eric

last: Verdin

institute: Buck Institute for Research on Aging

description: untreated vs. Nur77: 4 replicates

hyb_protocol: Ambion Gene TAC Hybstation. O/N at 42 degC in Ambion SlideHyb 2 buffer, 20%formamide, wash 42 degC in 2X SSC

scan_protocol: Axon 4000B scanner, data acquired with GenePix 6.0 software

data_processing: LOWESS and print-tip normalizations, median pixel values used, no background subtraction

source_name: DO11.10 T cell hybridoma, transduced with MSCV Nur77

label_protocol: Incorporation of aminoallyl-dUTP during cDNA first strand synthesis, followed by alkaline coupling to NHS-Cy3 and NHS-Cy5

extract_protocol: RNAsol total RNA extraction using acid phenol and guanidinium isothiocyanate, per Current Protocols in Molecular Biology

tag: cells spin-infected with MSCV IRES GFP retrovirus encoding Nur77

source_name: DO11.10 T cell hybridoma, untreated

tag: unmanipulated cells


title: Diffuse large B-cell lymphoma VUMC_L04_b32_s78


title: Diffuse large B-cell lymphoma VUMC_L08_b32_s82


title: slide 6 cy3 untreated cy5 Nur77

description: untreated vs. Nur77: 4 replicates


title: slide 8 cy5 untreated cy3 Nur77

description: untreated vs. Nur77: 4 replicates


title: slide 5 cy3 untreated cy5 Nur77

description: untreated vs. Nur77: 4 replicates


title: slide 3 cy5 untreated cy3 MSCV

description: untreated vs. empty virus: 4 replicates

source_name: DO11.10 T cell hybridoma, transduced with MSCV

tag: cells spin-infected with MSCV IRES GFP retrovirus


title: slide 22 cy 5 untreated  cy3 MEF2D-vp16

description: untreated vs. MEF2D-VP16: 4 replicates

source_name: DO11.10 T cell hybridoma, transduced with MEF2D-VP16

tag: cells spin-infected with MSCV IRES GFP retrovirus encoding activating MEF2D-VP16 fusion protein

tag: unmanipulated total thymocytes from balb/c DO11.10 TCR-transgenic mice


title: slide 2 cy3 untreated cy 5 MSCV

description: untreated vs. empty virus: 4 replicates


title: slide 15 cy5 DO11 untreated cy3 DO11 peptide-injected 12 hrs.

description: D011.10  thymocytes, uninjected vs. injected 12 hrs.: 6 replicates

source_name: DO11.10 total thymocytes, injected with antigenic peptide, 12h

source_name: DO11.10 total thymocytes


title: slide 1 cy3 untreated cy 5 MSCV

description: untreated vs. empty virus: 4 replicates


title: slide 4 cy5 untreated cy3 MSCV

description: untreated vs. empty virus: 4 replicates


title: slide 12 cy 5 untreated  cy3 MEF2D-vp16

description: untreated vs. MEF2D-VP16: 4 replicates


title: slide 16 cy5 DO11 untreated cy3 DO11 peptide-injected 12 hrs.


title: slide 14  cy3 DO11 untreated cy5 DO11 peptide-injected 12 hrs.

tag: total thymocytes from balb/c DO11.10 TCR-transgenic mice, 12 hours after ip injection of antigenic petide


title: Diffuse large B-cell lymphoma VUMC_L13_b32_s84


title: slide 11 cy 3 untreated  cy5 MEF2D-vp16

description: untreated vs. MEF2D-VP16: 4 replicates


title: slide 13-7 cy3 DO11 untreated cy5 DO11 peptide-injected 12 hrs.


title: slide 13 cy3 DO11 untreated cy5 DO11 peptide-injected 12 hrs.


title: slide 13-6 cy5 do11 untreated cy3 doll peptide-injected 6 hrs.

description: D011.10  thymocytes, uninjected vs. injected 6 hrs.: 6 replicates

source_name: DO11.10 total thymocytes, injected with antigenic peptide, 6h

tag: total thymocytes from balb/c DO11.10 TCR-transgenic mice, 6 hours after ip injection of antigenic petide


title: slide 11 cy5 do11 untreated cy3 doll peptide-injected 6 hrs.


title: slide 12 cy5 do11 untreated cy3 doll peptide-injected 6 hrs.


title: slide 21 cy 3 untreated  cy5 MEF2D-vp16

description: untreated vs. MEF2D-VP16: 4 replicates


title: slide 13-8 cy5 DO11 untreated cy3 DO11 peptide-injected 12 hrs.


title: slide 10 cy3 do11 untreated cy5 doll peptide-injected 6 hrs.


title: slide 9 cy3 do11 untreated cy5 doll peptide-injected 6 hrs.


title: slide 13-5 cy3 do11 untreated cy5 doll peptide-injected 6 hrs.


title: slide 13-8 cy5 DO11 untreated cy3 DO11 peptide-injected 3 hrs.

description: D011.10  thymocytes, uninjected vs. injected 3 hrs.: 6 replicates

source_name: DO11.10 total thymocytes, injected with antigenic peptide, 3h

tag: total thymocytes from balb/c DO11.10 TCR-transgenic mice, 3 hours after ip injection of antigenic petide


title: slide 13-5 cy3 DO11 untreated cy5 DO11 peptide-injected 3 hrs.


title: slide 13-6 cy3 DO11 untreated cy5 DO11 peptide-injected 3 hrs.


title: slide 17 cy3 mhc -/- cy5 do11 untreated

description: D011.10 vs. mhc ko thymocytes: 6 replicates

source_name: mhc -/- total thymocytes

tag: unmanipulated total thymocytes from c57 BL/6 mhc-deficient mice


title: slide 18 cy3 do11 untreated cy5 mhc -/-


title: slide 13-7 cy5 DO11 untreated cy3 DO11 peptide-injected 3 hrs.


title: slide 13-3 cy3 DO11 untreated cy5 DO11 peptide-injected 3 hrs.


title: slide 13-4 cy5 DO11 untreated cy3 DO11 peptide-injected 3 hrs.


title: slide 2 cy3 do11 untreated cy5 mhc -/-


title: slide 4 cy5 do11 untreated cy3 mhc -/-


title: slide 3 cy5 do11 untreated cy3 mhc -/-


title: slide 1 cy3 do11 untreated cy5 mhc -/-


title: slide 14-18 cy 5 untreated cy3 HDAC7 DP PMA/iono

description: untreated vs. HDAC7 DP, pma/ionomycin treated: 8 replicates

source_name: DO11.10 T cell hybridoma, transduced with MSCV HDAC7 DP, PMA/ionomycin treated 2.5h

tag: cells spin-infected with MSCV IRES GFP retrovirus encoding signal-refractory HDAC7 mutant and treated with PMA/ionomycin 2.5 hours


title: slide 15-18 cy 5 untreated cy3 HDAC7 DP PMA/iono


title: slide 15-17 cy 3 untreated cy5 HDAC7 DP PMA/iono


title: slide 14-17 cy 3 untreated cy 5 HDAC7 DP PMA/iono


title: slide 15-19 cy 3 untreated cy5 HDAC7 DP PMA/iono


title: slide 15-20 cy 5 untreated cy3 HDAC7 DP PMA/iono


title: slide 14-20 cy 5 untreated cy3 HDAC7 DP PMA/iono


title: slide 15-14 cy 5 untreated cy 3 MSCV pma/iono

description: untreated vs. empty virus, pma/ionomycin treated: 8 replicates

source_name: DO11.10 T cell hybridoma, transduced with MSCV, PMA/ionomycin treated 2.5h

tag: cells spin-infected with MSCV IRES GFP retrovirus and treated with PMA/ionomycin 2.5 hours


title: slide 15-16 cy 5 untreated cy 3 MSCV pma/iono


title: slide 14-19 cy 3 untreated cy5 HDAC7 DP PMA/iono


title: slide 14- 11 cy3 untreated cy5 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates

source_name: DO11.10 T cell hybridoma, transduced with HDAC7-VP16

tag: cells spin-infected with MSCV IRES GFP retrovirus encoding activating HDAC7-VP16 fusion protein


title: slide 14-16 cy 5 untreated cy 3 MSCV pma/iono


title: slide 14-15 cy 3 untreated cy 5 MSCV pma/iono


title: slide 15- 9 cy3 untreated cy5 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 14-14 cy 5 untreated cy 3 MSCV pma/iono


title: slide 15- 8 cy5 untreated cy3 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 14-13 cy 3 untreated cy 5 MSCV pma/iono


title: slide 15-15 cy 3 untreated cy 5 MSCV pma/iono


title: slide 14- 12 cy5 untreated cy3 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15- 7 cy3 untreated cy5 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 14- 7 cy3 untreated cy5 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15- 11 cy3 untreated  cy 5 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15-13 cy 3 untreated cy 5 MSCV pma/iono


title: slide 14- 8 cy5 untreated cy3 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15- 12 cy5 untreated cy3 HDAC7-VP16

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15-10 cy3 HDAC7-VP16 cy5 untreated

description: untreated vs. HDAC7-VP16: 10 replicates


title: slide 15-5  cy3 MSCV cy5 untreated

description: untreated vs. empty virus: 12 replicates


title: slide 14-5 cy3 MSCV cy5 untreated


title: slide 15-6 cy3 MSCV cy5 untreated


title: Slide 14-3  cy3 untreated cy5 MSCV


title: slide 15-4 cy 3 MSCV cy5 untreated


title: Slide 15-3 cy3 untreated cy5 MSCV


title: slide 14-6 cy3 MSCV cy 5 untreated


title: Slide 14-4 cy3 MSCV cy5 untreated


title: Slide 15-2 cy3 untreated cy 5 MSCV


title: Slide 15-1 cy 3 untreated cy 5 MSCV


title: Slide 14-2 cy 3 untreated cy 5 MSCV


title: slide 14-1 cy3 untreated cy5 MSCV


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Stationary phase_biol rep 1

status: Public on Oct 01 2007

city: Haren

first: Andrzej

last: Lulko

address: Kerklaan 30

institute: University of Groningen

hyb_protocol: Panorama hybridisation solution (PRHY0001) by Sigma was used for hybridisation as described by the manufacturer, ie: 1. Rinse the blots in 50 ml 2x SSPE for 5 minutes. Drain and discard the solution. 2. Pre-warm the hybridization oven to 65°C. Warm the Hybridization Solution (Sigma-Genosys Cat. No. PRHY0001 or Kit Cat. No. PRLB0001) to 65°C for about 10 minutes prior to use. Add the appropriate quantity of salmon testes DNA to achieve a final concentration of 100 μg/ml, immediately prior to using the Hybridization Solution. 3. Pre-hybridize the Panorama gene array in 5 ml Hybridization Solution for at least 1 hour at 65°C, using roller bottles at 6 r.p.m. (or continuously agitate if using sealed bags). 4. Add the entire labeled cDNA generated from Part Two of this protocol to 3 ml Hybridization Solution. Heat at 90 – 95°C for 10 minutes in a water bath to denature the cDNA. 5. Decant and discard the Hybridization Solution from the pre-hybridized array. Add the denatured labeled cDNA in Hybridization Solution to the array in the roller bottle. 6. Hybridize overnight (12 – 18 hours) at 65°C. 7. Decant the hybridization solution and save for future use or discard appropriately. 8. Add 40 – 50 ml of Wash Solution to the roller bottle. Wash the array by inverting the roller bottle by-hand, at room temperature for 2 – 3 minutes. Decant and discard the Wash Solution in an appropriate manner for radioactive waste solutions. Note: An alternative wash method may be adopted for the arrays. Arrays may be washed in a suitably-sized plastic food container (dedicated for use with radioactive materials). Agitate the container on a rocking table or use a shaking water bath. 9. Repeat step 8 two more times. 10. Pre-warm the Wash Solution to 65°C. Add 80 – 100 ml Wash Solution to the roller bottle. Wash filters in the hybridization oven at 65°C for 20 minutes (6 r.p.m.). Decant and discard the Wash Solution to an appropriate radioactive waste container. 11. Repeat step 10 two more times. 12. Remove the array from the roller bottle (or the alternative washing container). Lay the array on a sheet of blotting paper. 13. Air-dry the array for 2 – 3 minutes. 14. Wrap the array in clear food wrap and subject to autoradiography using Cyclone phospho-imager screens (Packard) for ~2.5 days

scan_protocol: After hybridization and washing, Cyclone phospho-imager screens (Packard) were exposed for ~2 days and read out with the Cyclone at 300dpi.

data_processing: Duplicate spots were averaged in Array-Pro software (Media Cybernetics, Inc.) and the signal was normalized after background subtraction by calculation of the percentage of total signal per gene using Microsoft Excel. Outstandingly high signals (for example whole genomic DNA control spots which act as a positive control and always show very strong signals) were excluded from calculations of the total signal. Statistical significance of the obtained gene expression ratios was assessed by the Cyber-T program

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Stationary phase Bacillus subtilis 168 CssS knockout cells overproducing AmyQ

label_protocol: Reverse transcription was carried out in a total volume of 50 μl. Aliquots of 1 pmol of B.subtilis ORF-speci®c primers (Eurogentec) were mixed with 4 μg isolated RNA, incubated for 10 min at 70°C and cooled on ice. Subsequently, 10 μl of 5x concentrated First strand buffer (Gibco BRL), 5 vl 100mM DTT, 0.5 μl RNasin (Roche, 40 U/ml), 2.5 μl dNTP mixture (5 mM dATP, 5 mM dTTP, 5 mM dGTP, 0.1 mM dCTP) were added, and the total volume was adjusted to 42.5 μl with DEPC-treated water, and kept on ice. After addition of 5 ml [alfa-33P]dCTP, the mixture was incubated for 10 min at 25°C, before the addition of 2.5 ml SuperscriptII (Gibco BRL). Reverse transcription reaction was carried out for 2 h at 42°C, 15 min at 70°C, and was stopped by adding 2 μl 0.5 M EDTA, 2 μl 10% SDS, 6 μl 3 M NaOH and incubating for 30 min at 68°C. After neutralization with 6 μl 3 M HCl, the labeled cDNA was puri®ed on a Sephadex G-25 column (Roche). Incorporation of label was checked by scintillation counting.

growth_protocol: B. subtilis strains were grown in TY medium (1% tryptone, 0.5% yeast extract and 1% NaCl) at 37°C, 250 rpm containing the appropriate antibiotic: spectinomycin (100 μg/ml).

extract_protocol: RNA was isolated by spinning down 2 ml of culture (30 s Eppendorf centrifuge, 14 000 r.p.m., 4°C) and resuspending the pellet in 0.3 ml ice-cold growth medium (final volume 0.4 ml). The cell suspension was added to a screw cap Eppendorf tube containing 1.5 g glass beads (75±150 mm), 0.5 ml phenol:chloroform:isoamylalcohol (12:12:1), 50 μl 10% SDS and 50 μl 3M sodium acetate (pH 5.2). All solutions were prepared with diethylpyrocarbonate (DEPC)-treated water. After vortexing, the tube was frozen in liquid nitrogen and stored at ±80°C. Cells were broken by shaking for 8 min in a shake-it-baby (15). After 5 min centrifugation (Eppendorf centrifuge, 10 000 r.p.m., 4°C) the water phase (0.4 ml) was transferred to a clean tube containing 0.4 ml chloroform. After vortexing and centrifugation (2 min, Eppendorf centrifuge, 14 000 r.p.m., 4°C), the water phase was transferred to a clean tube and the RNA was isolated with a High Pure RNA Isolation Kit (Roche). RNA was eluted in 50 μl elution buffer and quanti®ed with GeneQuant (Amersham).

tag: Bacillus subtilis 168 CssS knockout containing pKTH10 plasmid


title: B. subtilis 168 containing pUB110_stationary phase_biol rep 1

source_name: Stationary phase Bacillus subtilis 168 cells

tag: Bacillus subtilis 168 containing pUB110 plasmid (empty vector control)


title: B. subtilis 168 containing pKTH10_Stationary phase_biol rep 3

source_name: Stationary phase Bacillus subtilis 168 cells overproducing AmyQ

tag: Bacillus subtilis 168 containing pKTH10 plasmid


title: B. subtilis 168 containing pKTH10_Stationary phase_biol rep 2


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Late exp_biol rep 1

source_name: Late exponential Bacillus subtilis 168 CssS knockout cells overproducing AmyQ


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Late exp_biol rep 2


title: B. subtilis 168 containing pUB110_stationary phase_biol rep 3


title: B. subtilis 168 containing pKTH10_Late exp_biol rep 3

source_name: Late exponential Bacillus subtilis 168 cells overproducing AmyQ


title: Thymus_rep3

status: Public on Sep 30 2007

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

description: Third replicate of NeuroTrans_UMR7637 hybridization performed with 15µg of thymus RNA

hyb_protocol: NeuroTrans_UMR7637 microarrays were incubated at 50°C, 15 minutes in Tris 10m M pH 9, 0.1% SDS, 0.3% éthanolamine followed by 15 minutes in 4X SSC, 0,1% SDS.Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 15 hours. Microarrays were then washed at room temperature 2 minutes in 2X SSC, 0.1% SDS, 1 minute in 0.2X SSC and 2 minutes in 0.1X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Lite (Packard Biochip). Median signal and median local background intensities were extracted from the images using Imagene 4.2 software (Biodiscovery, Inc.)

data_processing:
Because the matrix has been spotted in duplicate on the array, we first calculated the mean signal and mean background values for each spot.
Signal-Background differences were then calculated for each spot in each experiment.
For comparing experiments, the sum of S-B values for each slide was then multiplied by a correcting factor so that the sum of the corrected ratios was equal in all experiments.

source_name: Tissue : thymus

label_protocol:
Fifteen µg of RNA were labelled with Cy5 by reverse transcription into cDNAs using random hexanucleotides (7.5 µM), 10 µM  DTT, 125 µM dNTP, 25 µM  dUTP-cy5 (Amersham) and 400 U of Superscript II (Invitrogen).
Labelled targets were then purified on  Qiaquick PCR purification columns (Qiagen) according to the manusfacturer’s instructions.

extract_protocol:
Total RNA was extracted from 5 thymus of B10D2 mice and treated with DNAse using RNeasy kit (Qiagen) according to the manusfacturer’s instructions.
Equal amounts of each RNA were pooled to obtain 15µg for microarray hybridization.

tag: Strain

value: B10D2, Age :Adult, Tissue :thymus