title: B. subtilis 168 containing pKTH10_Stationary phase_biol rep 1


title: B. subtilis 168 containing pUB110_Late exp_biol rep 3

status: Public on Oct 01 2007

type: RNA

city: Haren

first: Andrzej

last: Lulko

address: Kerklaan 30

country: Netherlands

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

molecule: total RNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Late exponential Bacillus subtilis 168 cells

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 containing pUB110 plasmid (empty vector control)


title: B. subtilis 168 containing pKTH10_Late exp_biol rep 1

source_name: Late exponential Bacillus subtilis 168 cells overproducing AmyQ

tag: Bacillus subtilis 168 containing pKTH10 plasmid


title: Thymus_rep2

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: Second 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.

organism: Mus musculus

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


title: B. subtilis 168 containing pKTH10_Late exp_biol rep 2


title: Cortex_rep3

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

source_name: Tissue : cortex

extract_protocol:
Total RNA was extracted from 6 cortex 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.

value: B10D2, Age :Adult, Tissue :cortex


title: B. subtilis 168 containing pUB110_Late exp_biol rep 2


title: Thymus_rep1

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


title: Cortex_rep2

description: Second replicate of NeuroTrans_UMR7637 hybridization performed with 15µg of cortex RNA


title: Cy3: sorted cells; high affinity to 2-NBDglucose; D=0.160 h-1 ;Cy5: untreated cells harvested at D=0.160 h-1

city: Leipzig

first: Jeannette

last: Achilles

address: Permoserstraße 15

department: Environmental Microbiology

country: Germany

institute: Helmholtz-Centre for Environmental Research - UFZ

description: Gene expression of a vital, stained and sorted subpopulation of Saccharomyces cerevisiae with high affinity to glucose, harvested at a dilution rate of D=0.160 h-1, and of cells from the whole population without further treatment grown at the same dilution rate were analysed.

hyb_protocol: The differently labelled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Processed Data: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized and united. An outliertest has been applied in order to find outliers amongst the gene replicats.  Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

organism: Saccharomyces cerevisiae

label_protocol:
The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3 signals of microarray detection.
6 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Fluorescein-dCTP.

growth_protocol: Cells were continuously cultivated in a reactor in 1 l Schatzmann-medium at 30°C. The pH 5.4 was constantly kept by adding 1 M NaOH as required (controlled by a pH-electrode). The aeration rate was constant at 3 l of air/l of medium/minute and the stirrer velocity was 600 rpm.

extract_protocol: The isolation of RNA was accomplished by using lyticase to lyse the cells and the Qiagen RNeasy Mini Kit with some modifications within the manufacturers´ protocol.

treatment_protocol: Cells were vital stained and sorted in tubes, standing in a container filled with dry ice.

tag: Saccharomyces cerevisiae H155

label_protocol: The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy5 signals of microarray detection.  6 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Biotin-dCTP.

treatment_protocol: Cells were continuously grown at a dilution rate of D=0.160 h-1


title: Cortex_rep1

description: First replicate of NeuroTrans_UMR7637 hybridization performed with 15µg of cortex RNA


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Stationary phase_biol rep 2

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

tag: Bacillus subtilis 168 CssS knockout containing pKTH10 plasmid


title: B. subtilis 168 containing pUB110_stationary phase_biol rep 2

source_name: Stationary phase Bacillus subtilis 168 cells


title: sorted cells; high affinity to 2-NBDglucose; D=0.400 h-1 and D=0.160 h-1

description: Gene expression of a vital, stained and sorted subpopulation of Saccharomyces cerevisiae with high affinity to glucose, harvested at a dilution rate of D=0.160 h-1 and D=0.400 h-1 were analysed.

treatment_protocol: Cells were continuously grown at a dilution rate of D=0.400 h-1; vital stained and sorted in tubes, standing in a container filled with dry ice.

source_name: sorted cells; high affinity to 2-NBDglucose; D=0.160 h-1

treatment_protocol: Cells were continuously grown at a dilution rate of D=0.160 h-1; vital stained and sorted in tubes, standing in a container filled with dry ice.


title: PAO1 minimal media phosphatidylcholine replicate 3

status: Public on Aug 15 2007

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

country: USA

institute: University of Hawaii at Manoa

description: Samples processed at Greenwood Biotechnology Facility (Honolulu, HI)

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: Signal Values determined using MAS 5

label: Biotin

organism: Pseudomonas aeruginosa

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

growth_protocol: 1x M9 minimal media supplemented with 0.4% phosphatidylcholine

extract_protocol: Pseudomonas aeruginosa total RNA isolation protocol developed by S. Lory and cleaned up with QIAgen RNease with extra on-column DNaseI treatment

tag: Pseudomonas aeruginosa strain PAO1


title: PAO1 minimal media phosphatidylcholine replicate 2


title: PAO1 minimal media phosphatidylcholine replicate 1


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Late exp_biol rep 3

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


title: CF Sputum in vivo replicate1

data_processing: Signal Values determined using MAS5

source_name: CF Sputum in vivo replicate1

growth_protocol: 1x M9 minimal media supplemented with 20 mM citrate

extract_protocol: TRIzol treated Pseudomonas aeruginosa total RNA was isolated according to protocol developed by S. Lory, and cleanded up with QIAgen RNeasy with extra oncolumn DNase I treatment

treatment_protocol: Sputum samples were maintained on ice at all times.  Sputum was treated with Sputolysin, proteinase K, DNase I, and pelleted.  Cell pellet was washed twice with COLD double distilled water.  Cell pellet was then resuspended in TRIzol reagent and sonicated for 10 secs at maximum level three times.  All genetic material was then phenol:chloroform extracted and ethanol precipitated, resuspended in DEPC-treated water and processed as per S. Lory protocol.

tag: Pseudomonas aeruginosa total RNA was isolated directly from CF sputum patient 42


title: CF Sputum in vivo replicate2

source_name: CF Sputum in vivo replicate2


title: CF Sputum pool isolate minimal media citrate replicate2

extract_protocol: Pseudomonas aeruginosa total RNA isolation protocol developed by S. Lory, and cleanded up with QIAgen RNeasy with extra oncolumn DNase I treatment

treatment_protocol: Sputum samples were maintained on ice at all times.  Sputum was treated with Sputolysin, proteinase K, DNase I, and pelleted.  Cell pellet was washed twice with COLD double distilled water and a 100 ul aliquot plated on PIA media for generation of a pool to be stored for in vitro studies.  Colonies were pooled and grown for 1 hr in PIA and then frozen away at -80 in small 250 ul aliquots.  One aliquot was used for each GeneChip study.

tag: A pool of Pseudomonas aeruginosa was purified from CF sputum patient 42 and grown in minimal media with 20 mM citrate.  This is our in vitro grown sample.


title: CF Sputum pool isolate minimal media citrate replicate3


title: PAO1 minimal media palmitate replicate 3

growth_protocol: 1x M9 minimal media supplemented with 0.4% palmitic acid


title: PAO1 minimal media palmitate replicate 2


title: Vibrio fischeri cells grown to an OD600 of 1.5 with exogenous 3OC6-HSL added #1

status: Public on Aug 01 2007

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Vibrio fischeri GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix Microarray Suite was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Aliivibrio fischeri

source_name: Symbiotic bacterium Vibrio fischeri

extract_protocol: Vibrio fischeri cells were treated as described in the RNA Protect Bacteria Reagent Handbook (QIAGEN – Germantown, MD) using the enzymatic lysis protocol. RNA extraction and purification followed the RNeasy Mini Kit (QIAGEN) protocol including on-column DNase treatment.


title: Vibrio fischeri cells grown to an OD600 of 0.3 with exogenous 3OC6-HSL added #1

scan_protocol: As recommended by the manufacturer (Affymetrix)


title: CF Sputum pool isolate minimal media citrate replicate1

tag: A pool of Pseudomonas aeruignosa was purified from CF sputum patient 42 and grown in minimal media with 20 mM citrate.  This is our in vitro grown sample.


title: Vibrio fischeri cells grown to an OD600 of 1.5 with no exogenous 3OC6-HSL added #1

label_protocol: As recommended by the manufacturer (Affymetrix)


title: Vibrio fischeri cells grown to an OD600 of 0.3 with no exogenous 3OC6-HSL added #1


title: PAO1 minimal media citrate replicate2

source_name: PAO1 minimal media citrate replicate2


title: Vibrio fischeri cells grown to an OD600 of 1.5 with exogenous 3OC6-HSL added #2


title: Vibrio fischeri cells grown to an OD600 of 0.3 with exogenous 3OC6-HSL added #2


title: untreated cells harvested at D=0.160 h-1 and D=0.400 h-1

description: Gene expression of Saccharomyces cerevisiae harvested at a dilution rate of D=0.160 h-1 and D=0.400 h-1 respectively, were analysed.

treatment_protocol: Cells were continuously grown at a dilution rate of D=0.160 h-1.

source_name: untreated cells harvested at D=0.400 h-1

treatment_protocol: Cells were continuously grown at a dilution rate of D=0.400 h-1.


title: Vibrio fischeri cells grown to an OD600 of 0.3 with no exogenous 3OC6-HSL added #2


title: PAO1 minimal media palmitate replicate 1


title: PAO1 minimal media citrate replicate3

source_name: PAO1 minimal media citrate replicate3


title: Vibrio fischeri cells grown to an OD600 of 1.5 with no exogenous 3OC6-HSL added #2


title: PAO1 minimal media citrate replicate1

source_name: PAO1 minimal media citrate replicate1


title: B. subtilis 168_CssS::sp mutant containing pKTH10_Stationary phase_biol rep 3


title: EPI_ATR_1

status: Public on Jul 31 2007

type: genomic

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

hyb_protocol: For hybridization, 40 μg of human Cot-1 DNA (Invitrogen, Carlsbad, CA) was  added to 60 μl of labeled genomic DNA, the probe was transferred to a Microcon YM-30 filter and centrifuged at 12,000 rcf for 8 min at RT. The spin column was inverted in a new collection tube and centrifuged at 12,000 rcf for 2 min at RT. The eluted probe volume was adjusted to 18 μl with nuclease free water and the following were added: 2 μl of yeast tRNA (10 μg/μl, Invitrogen, Carlsbad, CA), 4 μl of Poly dA-Poly dT (10 μg/μl, Sigma-Aldrich, St. Louis, MO),  5.1 μl of 20X SSC and 0.9 μl of 10% SDS. The probe was denatured at 100° C for 3 min and centrifuged at 12,000 rcf for 10 sec. The probe was added directly to the microarray and a cover slip was placed carefully. Slides were hybridized overnight in DIE-TECH 1 or 5 slide hybridization chambers in a 65° C water bath. After hybridization, cover slips were removed by placing slides in 2x SSC / 0.03% SDS. Slides were then washed sequentially in the following order: 2x SSC / 0.03% SDS for 5 min, 1x SSC / 0.03% SDS for 5 min, and 0.2x SSC / 0.03% SDS for five minutes. Slides were given a final wash in 0.2x SSC for two minutes, and centrifuged dry at 500 rpm for 5 min.

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA).

data_processing: Images were gridded and spots were quantified using GenePix Pro 6.0 software (Axon Instruments, Union City, CA).

molecule: genomic DNA

organism: Homo sapiens

label_protocol: For each sample, 100 ng of normal genomic DNA was converted into a WGA library in a volume of 15 ul and amplified by PCR following the manufacturer’s WGA amplification protocol. Hundred ng aliquots of the products were then subjected to a second WGA PCR amplification in the presence of amino-allyl dUTP and purified. Yields after all WGA PCR amplifications were between 10 to 20 μg per reaction and used for the hybridizations. For all WGA amplified genomic DNA samples with aminoallyl dUTP incorporated (4 μg), nuclease free water was added to 500 μl, the sample was transferred to a Microcon YM-30 filter, and centrifuged at 12,000 rcf at RT for 12 minutes. The spin column was inverted in a new collection tube and centrifuged at 12,000 rcf for 2 min at RT. The amount of sample was measured and the volume was adjusted to 5 μl with nuclease free water. For labeling, 5 μl of 1 M sodium bicarbonate (pH 9.0) was added and allowed to incubate at RT for 10 min. Two μl of anhydrous DMSO were added to Alexa Fluor 647 (Cy5) and 555 (Cy3) dye packs (Invitrogen, Carlsbad, CA), mixed thoroughly, and 2 μl of the appropriate dye was added to each sample. The labeling mixture was incubated in the dark at RT for 1 hour. The reaction was stopped by the addition of 9 μl of 4 M Hydroxylamine and incubated in room temperature for 15 min. The Cy3 labeled and Cy5 labeled genomic DNA for each hybridization were mixed, and RNase free water was added to 100 μl, and purified using Qiaquick (Qiagen, Valencia, CA) spin columns.  The final eluted volume was 60 μl.

extract_protocol: Microdissection (LCM) was performed from frozen tissue sections with the SL Microtest device using μCUT software (MMI). Approximately 10,000 cells were captured for each sample. Serial sections were used if cells could not be obtained from a single section. Genomic DNA was isolated from the cells using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) and DNA concentration was determined using Quant-iT DNA Assay Kit, High Sensitivity (Invitrogen, Carlsbad, CA).

tag: Atrophic Epithelium - Simple Cystic Atrophy

source_name: Human Genomic DNA : Male

tag: Promega Normal Genomic DNA


title: MET_HR_12

tag: Metastatic Prostate Carcinoma


title: STROMA_ADJ_PCA_1a

tag: Normal Stroma - Adjacent Tumor (NAS)


title: PCA_27

tag: Prostate Carcinoma


title: WERI let-7 transfection

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

description: let-7 WERI transfection

hyb_protocol: Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate, pH 6.5, 33% formamide and 40 ug salmon sperm DNA), and hybridized on a rotating platform for 16-24 h at 42°C.

scan_protocol: Slides were washed (rocking ~30 seconds in 6x SSPE, 0.005% sarcosine, ~30 seconds in 0.06x SSPE) and scanned with an Axon 4000A microarray scanner (Axon Instruments, Union City, CA)

data_processing: TIFF images were quantitated with GenePix (Axon Instruments). Individual channels were spatially detrended (that is, overall correlations between spot intensity and position on the slide were removed) by high-pass filtering using 10% outliers. We applied variance stabilizing normalization (VSN) using 25% of the genes to normalize all single channels to each other. Measurements were transformed to arcsinh values (which are similar to natural log values, but are defined for negative numbers which emerge from the VSN).

source_name: human retinoblastoma Weri cells

label_protocol:
miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). In brief, for miRNA profiling, 7ug of DNAse treated (Fermentas) total RNA was chemically labeled with Ulysis Alexa Fluor 546/647 kits (Invitrogen) according to manufacturer’s instructions. For mRNA profiling, cDNA was generated and labeled as described (Zhang et al., 2004).
Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR. Probing microRNAs with microarrays: tissue specificity and functional inference.
RNA. 2004 Nov;10(11):1813-9. Erratum in: RNA. 2005 Jan;11(1):114, PMID: 15496526, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15496526
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR. The functional landscape of mouse gene expression. J Biol. 2004;3(5):21, PMID: 15588312, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15588312

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instructions.

tag: let-7 miRNAtransfection

label_protocol: same as for channel_1

extract_protocol: same as for channel_1

tag: scrambled let-7 miRNA control transfection


title: E12

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues.

hyb_protocol: Mixed labeled cDNAs were added to hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40 μg herring sperm DNA (Invitrogen, Carlsbad, USA). Hybridizations were carried out in a final volume of 0.5 ml injecting into an Agilent hybridization chamber at 42°C on a rotating platform in a hybridization oven (Robbins Scientific Corporation, Sunnyvale, USA) for 16–24 h. Slides were then washed (rocking for approximately 30 seconds in 6 × SSPE, 0.005% sarcosine, then rocking for approximately 30 seconds in 0.06 × SSPE) and scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA). Hybridizations were performed in duplicate with fluor reversal: that is, each mRNA sample was examined in duplicate, once in the Cy3 channel and once in the Cy5 channel, on separate arrays. Each array was hybridized with two samples simultaneously, each from an individual tissue.

scan_protocol: Slides were scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA).

data_processing: TIFF images were quantitated with GenePix 3.0 (Axon Instruments). Individual channels were spatially denoised (i.e., overall correlations between spot intensity and position on the slide removed) by using spatial trend removal (STR) with 10% outliers. We applied variance stabilizing normalization (VSN) by using 25% of the genes to normalize all single channels to each other. Finally, we manually identified and removed data from residual artifacts apparent on microarray images and measurements that showed high inconsistency between dye-swaps.

label: Cy3 or Cy5

molecule: polyA RNA

source_name: Pooled mouse CD1 strain E12

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with random nonamer primers (1 μg per reaction) and T18VN (0.25 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water. Purified cDNA was reacted with N-hydroxy succinimide esters of Cy3 or Cy5 (Amersham Pharmacia Biotech, Piscataway, USA) following the manufacturer's instructions.

extract_protocol: RNA was extracted using homogenization and Trizol reagent (Invitrogen, Carlsbad, USA) following the instructions from the manufacturer.

tag: Pooled mouse CD1 strain E12


title: PCA_26


title: let-7 WERI transfection fluor flip replicate

description: let-7 WERI transfection

label_protocol:
miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). In brief, for miRNA profiling, 7ug of DNAse treated (Fermentas) total RNA was chemically labeled with Ulysis Alexa Fluor 546/647 kits (Invitrogen) according to manufacturer’s instructions. For mRNA profiling, cDNA was generated and labeled as described (Zhang et al., 2004).
Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR. Probing microRNAs with microarrays: tissue specificity and functional inference.
RNA. 2004 Nov;10(11):1813-9. Erratum in: RNA. 2005 Jan;11(1):114, PMID: 15496526, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15496526

Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR. The functional landscape of mouse gene expression. J Biol. 2004;3(5):21, PMID: 15588312, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15588312


title: EPI_BPH_2

tag: BPH Epithelium


title: PCA_6


title: PCA_7


title: STROMA_NOR_3

tag: Normal Stroma - Organ Donor


title: B. subtilis 168 containing pUB110_Late exp_biol rep 1

source_name: Late exponential Bacillus subtilis 168 cells

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


title: STROMA_NOR_2


title: PIN_7

tag: Prostatic Intraepithelial Neoplasia


title: MET_HR_4


title: EPI_ATR_PIA3

tag: Proliferative inflammatory atrophy (PIA)


title: MET_HR_3


title: STROMA_EPIBPH_6

tag: Stroma - Epithelial BPH


title: MET_HR_2


title: MET_HR_6


title: PCA_24


title: MET_HR_5


title: PIN_12


title: PCA_28


title: EPI_ATR_2

tag: Atrophic Epithelium - Simple Atrophy


title: EPI_NOR_2

tag: Normal Epithelium - Organ Donor


title: STROMA_BPH_4

tag: Stromal BPH nodule


title: EPI_NOR_1


title: MET_HR_7


title: EPI_BPH_4


title: EPI_NOR_3


title: PIN_13


title: EPI_ATR_PIA4


title: EPI_ATR_PIA5


title: MET_HR_10


title: STROMA_BPH_7


title: MET_HR_11b


title: PCA_30


title: MET_HR_11a


title: PCA_29


title: MET_HN_2


title: MET_HR_9


title: WA25-64


title: MET_HR_14


title: STROMA_BPH_5


title: EPI_ADJ_PCA_8

tag: Normal Prostate Glands


title: PCA_4

tag: Promega Normal Genomic DNA


title: WA20-19a_0826

tag: Metastatic Prostate Carcinoma


title: PCA_17


title: WA20-19b_0901


title: EPI_BPH_3


title: PCA_2


title: PCA_15


title: PCA_22


title: MET_HR_13


title: MET_HN_1


title: PCA_16


title: MET_HR_1


title: IF 03-6613--99G PIN


title: PIN_4


title: PCA_21


title: PIN_8


title: PCA_1


title: STROMA_NOR_1


title: Listeria monocytogenes alkaline (ph 9.5) tolerance response

status: Public on Jul 25 2007

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description: Several controls were employed to minimise technical and biological variations, and ensure the quality of the data: i) each ORF was present in duplicate in each array, ii) each RNA preparation was used to make probes for at least two-separate arrays with reversal of incorporated dye and iii) three independent RNA batches from each condition were analysed.

hyb_protocol: Purified labelled L. monocytogenes cDNA from alkali treated and control samples were hybridised on microarray slides consisting of 6347 70-mer oligonucleotides representing Open Reading Frames (ORFs) from L. monocytogenes (Version 1) strains EGD-e, 4b F2365, 1/2a F6854 and 4b H7858, obtained from Pathogen Functional Genomic Research Centre (http://pfgrc.tigr.org). Before hybridization, microarray slides were pre-hybridized with pre-hybridization buffer at 42˚C for 45 min. Pre-hybridized slides were washed with water (4 times) and isopropanol (3 times) for 2 min each and dried by centrifugation. Purified probes were speed-vaced and resuspended in hybridization buffer. The probes in hybridization buffer were applied to the microarray slides covered with lifterslips (Erie Scientific Co.). Hybridized slides were sealed in a water tight hybridization chamber. These chambers were incubated for 14-16 h in a 42˚C water bath. Hybridized arrays were then washed 2 times with low stringency, medium stringency, and high stringency buffers for 10 min at room temperature using a reciprocal shaking table.

scan_protocol: Hybridised slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments) with Acuity 4.0 software and scans were stored as single TIFF images.

data_processing:
TIFF images of the hybridised arrays were analysed using the TIGR spotfinder software (www.tigr.org/software), and the local background was subsequently subtracted. The data set was normalised using the LOWESS algorithm by the TIGR-MIDAS (www.tigr.org/software) software. The normalized log2 ratio of test/controlsignal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (Significance-Analysis-of-Microarrays:
http://www-stat.stanford.edu/~tibs/SAM/) (Tusher et al., 2001)

organism: Listeria monocytogenes 10403S

source_name: Listeria monocytogenes control

label_protocol: cDNA was synthesized from the purified RNA by the Institute of Genomics Research microarray protocol (TIGR). In this process 2 μg of the purified RNA was annealed with random hexamers as primers (Invitrogen) (70°C/5min and snap frozen in ice/1min), and extended overnight at 42°C with SuperScript II reverse transcriptase (Invitrogen) in the presence of 0.1 M dithiothreitol 12.5 mM DNTP/aa-UTP (Ambion) mix. Residual RNA was removed and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then recovered, labelled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ), and purified, using Qiagen PCR purification kits following the manufacturers instructions.

growth_protocol: Hundred microlitres of an overnight grown Listeria monocytogenes 10403S culture were inoculated into a 250 ml Erlenmeyer flask with 100 ml of BHI, and cultures were incubated at 30° C with shaking at 200 rpm. Cells were harvested by centrifugation when the optical density at 600 nm reached ~0.4, and then rapidly transferred to prewarmed (30 ° C) BHI (Control cultures) for 60 min.

extract_protocol: RNA was extracted from samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

tag: Listeria monocytogenes strain 10403S

source_name: Listeria monocytogenes alkaline (pH 9.5) treated cells

extract_protocol: RNA was extracted using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

treatment_protocol: Hundred microlitres of an overnight grown Listeria monocytogenes 10403S culture were inoculated into a 250 ml Erlenmeyer flask with 100 ml of BHI, and cultures were incubated at 30° C with shaking at 200 rpm. Cells were harvested by centrifugation when the optical density at 600 nm reached ~0.4, and then rapidly transferred to prewarmed (30 ° C) alkali adjusted BHI pH 9.5 (Adapted cultures) for 60 min. The pH of BHI medium was adjusted to 9.5 with a glycine-NaOH-NaCl buffer.


title: PCA_9

tag: Prostate Carcinoma


title: Listeria monocytogenes alkaline (ph 9.0) shock 30 min

hyb_protocol: Purified labelled L. monocytogenes cDNA from alkali treated and control samples were hybridised on microarray slides consisting of 6347 70-mer oligonucleotides representing Open Reading Frames (ORFs) from L. monocytogenes (Version 1) strains EGD-e, 4b F2365, 1/2a F6854 and 4b H7858, obtained from Pathogen Functional Genomic Research Centre (http://pfgrc.tigr.org).  Before hybridization, microarray slides were pre-hybridized with pre-hybridization buffer at 42˚C for 45 min.  Pre-hybridized slides were washed with water (4 times) and isopropanol (3 times) for 2 min each and dried by centrifugation.  Purified probes were speed-vaced and resuspended in hybridization buffer. The probes in hybridization buffer were applied to the microarray slides covered with lifterslips (Erie Scientific Co.).  Hybridized slides were sealed in a water tight hybridization chamber. These chambers were incubated for 14-16 h in a 42˚C water bath. Hybridized arrays were then washed 2 times with low stringency, medium stringency, and high stringency buffers for 10 min at room temperature using a reciprocal shaking table.

data_processing:
TIFF images of the hybridised arrays were analysed using the TIGR spotfinder software (www.tigr.org/software), and the local background was subsequently subtracted. The data set was normalised using the LOWESS algorithm by the TIGR-MIDAS (www.tigr.org/software) software. The normalized log2 ratio of test/controlsignal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimatelycalculated. Significant changes of gene expression were identified with SAM (Significance-Analysis-of-Microarrays:
http://www-stat.stanford.edu/~tibs/SAM/) (Tusher et al., 2001)

label: Cy3. Cy5 in flip dye experiment

source_name: Listeria monocytogenes 10403S

extract_protocol: RNA was extracted from AS and AA samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

label: Cy5. Cy3 in flip dye experiment

source_name: Listeria monocytogenes 10403S alkaline (ph 9.0) treated cells

treatment_protocol:
Overnight cultures of L. monocytogenes 10403S were inoculated (1:100) into 20 ml of BHI (pH 7) in a 50 ml Erlenmeyer flask, and incubated at 30°C with shaking at 200 rpm. Growth was monitored by measuring OD600, using a Beckman DU-65 spectrophotometer.
Cells to be subjected to alkali shock (AS) were harvested by centrifugation (8,000g x10min at 4°C) from 20 ml of this culture when the optical density at 600 nm reached 0.4. Recovered cells were washed, and immediately resuspended in 20 ml pre-warmed (30°C) pH 9 MBHI (test) or neutral MBHI (pH 7 control) for 15, 30 or 60 min.


title: Listeria monocytogenes alkaline shock (pH 9.0) 60 min

organism: Listeria monocytogenes

source_name: Listeria monocytogenes 10403S  60 min alkaline (ph 9.0) shocked cells


title: Listeria monocytogenes alkaline (pH 9.0) Adaptation Response

hyb_protocol: Purified labelled L. monocytogenes cDNA from alkali adapted and control samples were hybridised on microarray slides consisting of 6347 70-mer oligonucleotides representing Open Reading Frames (ORFs) from L. monocytogenes (Version 1) strains EGD-e, 4b F2365, 1/2a F6854 and 4b H7858, obtained from Pathogen Functional Genomic Research Centre (http://pfgrc.tigr.org). Before hybridization, microarray slides were pre-hybridized with pre-hybridization buffer at 42˚C for 45 min. Pre-hybridized slides were washed with water (4 times) and isopropanol (3 times) for 2 min each and dried by centrifugation. Purified probes were speed-vaced and resuspended in hybridization buffer. The probes in hybridization buffer were applied to the microarray slides covered with lifterslips (Erie Scientific Co.). Hybridized slides were sealed in a water tight hybridization chamber. These chambers were incubated for 14-16 h in a 42˚C water bath. Hybridized arrays were then washed 2 times with low stringency, medium stringency, and high stringency buffers for 10 min at room temperature using a reciprocal shaking table.

tag: Listeria monocytogenes 10403S

source_name: Listeria monocytogenes 10403S alkaline adapted cells

extract_protocol: RNA was extracted from AA samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

treatment_protocol: Overnight cultures of L. monocytogenes 10403S were inoculated (1:100) into 20 ml of BHI (pH 7) in a 50 ml Erlenmeyer flask, and incubated at 30°C with shaking at 200 rpm. Growth was monitored by measuring OD600, using a Beckman DU-65 spectrophotometer.  Cells to be examined in terms of alkali adaptation (AA) were produced by inoculation of the overnight culture (1:100) into 20ml of MBHI adjusted at pH 9 (test) or pH 7 (control), and incubation at 30°C until they reached OD600 0.4.


title: Listeria monocytogenes alkaline shock (pH 9.0 ) for 15 min

data_processing:
TIFF images of the hybridised arrays were analysed using the TIGR spotfinder software (www.tigr.org/software), and the local background was subsequently subtracted. The data set was normalised using the LOWESS  algorithm by the TIGR-MIDAS (www.tigr.org/software) software. The normalized log2 ratio of test/control signal for each spot was recorded. The averaged log2 ratio for each gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (Significance-Analysis-of-Microarrays:
http://www-stat.stanford.edu/~tibs/SAM/) software using one class mode.

label: Cy3. Cy5 for flip dye experiment

source_name: Listeria monocytogenes 10403S alkaline shock control RNA

extract_protocol: RNA was extracted from control and alkaline shock (AS) samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

label: Cy5. Cy3 in flip dye experiment.

source_name: Listeria monocytogenes 10403S alkaline shocked RNA


title: H37Ra vs H37Rv 1year #2.5

status: Public on Jul 05 2007

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: color swap (+) polarity

hyb_protocol: Fluoroscently labeled cDNAs (5 µg each) were pooled, heat denatured and mixed with hybridization buffer SlideHyb #1 (Ambion).  Hybridization was performed in a humidified hybridization chamber for 16 h submerged in a 50°C water bath with LifterSlipsTM (Erie Scientific). Slides were washed twice with the first and low stringency washing buffer (2 × SSC, 0.1% SDS) for 10 min at 50°C, followed by 2 × of the second washing buffer (0.5 × SSC, 0.1% SDS) for 10 min at 50°C and the third washing buffer (0.05 × SSC) for 4 min at 25°C.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Image Analysis / Feature Extraction software G2567AA (Version A.7.5.1) using almost default settings for microarrays loaded with a grid file, except that the constant coefficient of variation for features and background was raised 5 fold. Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The log intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

data_processing: Data analysis was performed with ResolverBiosoftware, Build 5.1.0.0.163 (Rosetta Biosoftware).

organism: Mycobacterium tuberculosis H37Ra

source_name: H37Ra 1year #2.5

label_protocol: Total RNA (5µg of early log, log and stationary phase) or amplified RNA (1year) were directly labeled with Cy3-dUTP or Cy5-dUTP using LabelStar Array kit (Qiagen). Only 1year samples were amplified as described (Rachman et al., J Biotechnol. 2006 Oct 20;126(1):61-8).

growth_protocol: M. tuberculosis H37Ra ATCC 25177 was used as test strain and M. tuberculosis H37Rv served as reference strain and was kindly provided by Stewart Cole (Institut Pasteur, Paris, France). Mycobacterial strain stocks were inoculated in 100ml 7H9 medium supplemented with 10% (vol/vol) albumin-dextrose-catalase enrichment (Difco Laboratories) and 0.05% (vol/vol) Tween 80 (Sigma) and grown to defined time point at 37°C. Bacterial strains were cultured in roller bottles with a rolling speed of 5 rpm. For the 1-year culture sample, cultures were transferred to 50 ml tubes to the full, sealed withParafilm tightly after 2 weeks incubation in roller bottles and incubated at 37°C.

extract_protocol: Total RNA from mycobacterial cells were prepared as described (Dietrich et al., FEMS Microbiol Lett. 2000 May 15;186(2):177-80)

treatment_protocol: untreated

tag: biological sample 2, technical replicate 5

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv 1year #2.5


title: H37Rv vs H37Ra 1year #2.3

description: color swap (-) polarity

source_name: H37Rv 1year #2.3

tag: biological sample 2, technical replicate 3

source_name: H37Ra 1year #2.3


title: H37Rv vs H37Ra 1year #2.2

description: color swap (-) polarity

source_name: H37Rv 1year #2.2

tag: biological sample 2, technical replicate 2

source_name: H37Ra 1year #2.2


title: H37Ra vs H37Rv 1year #2.4

description: color swap (+) polarity

source_name: H37Ra 1year #2.4

tag: biological sample 2, technical replicate 4

source_name: H37Rv 1year #2.4


title: H37Ra vs H37Rv 1year #2.6

description: color swap (+) polarity

source_name: H37Ra 1year #2.6

tag: biological sample 2, technical replicate 6

source_name: H37Rv 1year #2.6


title: H37Rv vs H37Ra 1year #2.1

description: color swap (-) polarity

source_name: H37Rv 1year #2.1

tag: biological sample 2, technical replicate 1

source_name: H37Ra 1year #2.1


title: H37Ra vs H37Rv 1year #1.6.2

description: color swap (+) polarity

tag: biological sample 1, technical replicate 6.2


title: 293shM1

city: siena

first: alessio

last: zippo

address: via fiorentina 1

country: Italy

institute: university of siena

description: RNA

hyb_protocol: see manufacturer's web site at http://www.agilent.com/

scan_protocol: Scanned by G2565BA DNA Scanner Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized. background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from human 293 T-Rex cells expression shRNA shsMYC-1 labeled with Cyanine-5 (red).

growth_protocol: Human 293 T-rex cell line. provided by Invitrogen were maintained in cell culture medium containing DMEM. 10% FCS. penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shcM-1.  The cells were synchronized at confluence for 4 days in DMEM. 10% FSC and then stimulated with 50% horse serum for 120 minutes.

extract_protocol: TriZol procedure

tag: 293 T-rex cell line

source_name: Total RNA from human 293 T-Rex cells expression shRNA shMYC-1 labeled with Cyanine-3 (green).

growth_protocol: Human 293 T-rex cell line. provided by Invitrogen were maintained in cell culture medium containing DMEM. 10% FCS. penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shMYC-1.  The cells were synchronized  for 4 days in DMEM 10% FSC and then stimulated with 50% horse serum for 120 minutes.


title: 293shMYC-2

description: RNA

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from human 293 T-Rex cells expression shRNA shsMYC-2 labeled with Cyanine-5 (red).

label_protocol: see manufacturer's web site at http://www.agilent.com/

growth_protocol: Human 293 T-rex cell line, provided by Invitrogen were maintained in cell culture medium containing DMEM, 10% FCS, penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shcM-2.  The cells were synchronized at confluence for 4 days in DMEM. 10% FSC and then stimulated with 50% horse serum for 120 minutes.

source_name: Total RNA from human 293 T-Rex cells expression shRNA shMYC-2 labeled with Cyanine-3 (green).

growth_protocol: Human 293 T-rex cell line, provided by Invitrogen were maintained in cell culture medium containing DMEM, 10% FCS, penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shMYC-2.  The cells were synchronized  for 4 days in DMEM 10% FSC and then stimulated with 50% horse serum for 120 minutes.


title: H37Ra vs H37Rv 1year #1.6

description: color swap (+) polarity

source_name: H37Ra 1year #1.6

tag: biological sample 1, technical replicate 6

source_name: H37Rv 1year #1.6


title: 293shP2

description: RNA

source_name: Total RNA from human 293 T-Rex cells expression shRNA shsPIM1-2 labeled with Cyanine-5 (red).

growth_protocol: Human 293 T-rex cell line, provided by Invitrogen were maintained in cell culture medium containing DMEM, 10% FCS, penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shcP-2.  The cells were synchronized at confluence for 4 days in DMEM. 10% FSC and then stimulated with 50% horse serum for 120 minutes.

source_name: Total RNA from human 293 T-Rex cells expression shRNA shPIM1-2 labeled with Cyanine-3 (green).

growth_protocol: Human 293 T-rex cell line, provided by Invitrogen were maintained in cell culture medium containing DMEM, 10% FCS, penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shPIM1-2.  The cells were synchronized  for 4 days in DMEM 10% FSC and then stimulated with 50% horse serum for 120 minutes.


title: 293shP1

description: RNA

source_name: Total RNA from human 293 T-Rex cells expression shRNA shsPIM1-1 labeled with Cyanine-5 (red).

growth_protocol: Human 293 T-rex cell line. provided by Invitrogen were maintained in cell culture medium containing DMEM. 10% FCS. penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shcP-1.  The cells were synchronized at confluence for 4 days in DMEM. 10% FSC and then stimulated with 50% horse serum for 120 minutes.

source_name: Total RNA from human 293 T-Rex cells expression shRNA shPIM1-1 labeled with Cyanine-3 (green).

growth_protocol: Human 293 T-rex cell line. provided by Invitrogen were maintained in cell culture medium containing DMEM. 10% FCS. penicillin/streptomycin/amphotericin B.Cells were transfected with DNA constructs expressing shRNA shPIM1-1.  The cells were synchronized  for 4 days in DMEM 10% FSC and then stimulated with 50% horse serum for 120 minutes.


title: H37Ra vs H37Rv 1year #1.5

description: color swap (+) polarity

source_name: H37Ra 1year #1.5

tag: biological sample 1, technical replicate 5

source_name: H37Rv 1year #1.5


title: H37Ra vs H37Rv 1year #1.4

description: color swap (+) polarity

source_name: H37Ra 1year #1.4

tag: biological sample 1, technical replicate 4

source_name: H37Rv 1year #1.4


title: H37Rv vs H37Ra 1year #1.3.2

description: color swap (-) polarity

tag: biological sample 1, technical replicate 3.2


title: H37Rv vs H37Ra 1year #1.3

description: color swap (-) polarity

source_name: H37Rv 1year #1.3

tag: biological sample 1, technical replicate 3

source_name: H37Ra 1year #1.3


title: H37Rv vs H37Ra 1year #1.2

description: color swap (-) polarity

source_name: H37Rv 1year #1.2

tag: biological sample 1, technical replicate 2

source_name: H37Ra 1year #1.2


title: H37Ra vs H37Rv stationay pahse #2.6

description: color swap (+) polarity

source_name: H37Ra stationay pahse #2.6

tag: stationay pahse

source_name: H37Rv stationay pahse #2.6


title: H37Rv vs H37Ra 1year #1.1

description: color swap (-) polarity

source_name: H37Rv 1year #1.1

tag: biological sample 1, technical replicate 1

source_name: H37Ra 1year #1.1


title: H37Ra vs H37Rv stationay pahse #2.4

description: color swap (+) polarity

source_name: H37Ra stationay pahse #2.4

source_name: H37Rv stationay pahse #2.4


title: H37Rv vs H37Ra stationay pahse #2.3

description: color swap (-) polarity

source_name: H37Rv stationay pahse #2.3

source_name: H37Ra stationay pahse #2.3


title: H37Rv vs H37Ra stationay pahse #2.1

description: color swap (-) polarity

source_name: H37Rv stationay pahse #2.1

source_name: H37Ra stationay pahse #2.1


title: PCA_8

tag: Prostate Carcinoma

source_name: Human Genomic DNA : Male

tag: Promega Normal Genomic DNA


title: H37Ra vs H37Rv stationay pahse #1.5

description: color swap (+) polarity

source_name: H37Ra stationay pahse #1.5

source_name: H37Rv stationay pahse #1.5


title: H37Rv vs H37Ra stationay pahse #2.2

description: color swap (-) polarity

source_name: H37Rv stationay pahse #2.2

source_name: H37Ra stationay pahse #2.2


title: H37Ra vs H37Rv stationay pahse #2.5

description: color swap (+) polarity

source_name: H37Ra stationay pahse #2.5

tag: biological sample 2, technical replicate 5

source_name: H37Rv stationay pahse #2.5


title: H37Ra vs H37Rv stationay pahse #1.4

description: color swap (+) polarity

source_name: H37Ra stationay pahse #1.4

source_name: H37Rv stationay pahse #1.4


title: H37Ra vs H37Rv stationay pahse #1.6

description: color swap (+) polarity

source_name: H37Ra stationay pahse #1.6

source_name: H37Rv stationay pahse #1.6


title: H37Rv vs H37Ra stationay pahse #1.2

description: color swap (-) polarity

source_name: H37Rv stationay pahse #1.2

source_name: H37Ra stationay pahse #1.2


title: H37Ra vs H37Rv log phase #2.6

description: color swap (+) polarity

source_name: H37Ra log phase #2.6

tag: log phase

source_name: H37Rv log phase #2.6


title: H37Rv vs H37Ra stationay pahse #1.1

description: color swap (-) polarity

source_name: H37Rv stationay pahse #1.1

source_name: H37Ra stationay pahse #1.1


title: H37Rv vs H37Ra stationay pahse #1.3

description: color swap (-) polarity

source_name: H37Rv stationay pahse #1.3

source_name: H37Ra stationay pahse #1.3


title: H37Rv vs H37Ra log phase #2.2

description: color swap (-) polarity

source_name: H37Rv log phase #2.2

tag: biological sample 2, technical replicate 2

source_name: H37Ra log phase #2.2


title: H37Rv vs H37Ra log phase #2.3

description: color swap (-) polarity

source_name: H37Rv log phase #2.3

tag: biological sample 2, technical replicate 3

source_name: H37Ra log phase #2.3


title: H37Ra vs H37Rv log phase #2.4

description: color swap (+) polarity

source_name: H37Ra log phase #2.4

tag: biological sample 2, technical replicate 4

source_name: H37Rv log phase #2.4


title: H37Ra vs H37Rv log phase #2.5

description: color swap (+) polarity

source_name: H37Ra log phase #2.5

source_name: H37Rv log phase #2.5


title: H37Rv vs H37Ra log phase #2.1

description: color swap (-) polarity

source_name: H37Rv log phase #2.1

tag: biological sample 2, technical replicate 1

source_name: H37Ra log phase #2.1


title: H37Ra vs H37Rv log phase #1.4

description: color swap (+) polarity

source_name: H37Ra log phase #1.4

source_name: H37Rv log phase #1.4


title: H37Rv vs H37Ra log phase #1.3

description: color swap (-) polarity

source_name: H37Rv log phase #1.3

source_name: H37Ra log phase #1.3


title: H37Rv vs H37Ra log phase #1.1

description: color swap (-) polarity

source_name: H37Rv log phase #1.1

source_name: H37Ra log phase #1.1


title: H37Ra vs H37Rv log phase #1.5

description: color swap (+) polarity

source_name: H37Ra log phase #1.5

source_name: H37Rv log phase #1.5


title: H37Rv vs H37Ra log phase #1.2

description: color swap (-) polarity

source_name: H37Rv log phase #1.2

source_name: H37Ra log phase #1.2


title: H37Rv vs H37Ra early log phase #2.2

description: color swap (-) polarity

source_name: H37Rv early log phase #2.2

tag: early log phase

source_name: H37Ra early log phase #2.2


title: H37Rv vs H37Ra early log phase #1.2

description: color swap (-) polarity

source_name: H37Rv early log phase #1.2

source_name: H37Ra early log phase #1.2


title: H37Ra vs H37Rv early log phase #2.6

description: color swap (+) polarity

source_name: H37Ra early log phase #2.6

tag: biological sample 2, technical replicate 6

source_name: H37Rv early log phase #2.6


title: H37Rv vs H37Ra early log phase #2.1

description: color swap (-) polarity

source_name: H37Rv early log phase #2.1

source_name: H37Ra early log phase #2.1


title: H37Ra vs H37Rv early log phase #2.5

description: color swap (+) polarity

source_name: H37Ra early log phase #2.5

source_name: H37Rv early log phase #2.5


title: H37Rv vs H37Ra early log phase #1.3

description: color swap (-) polarity

source_name: H37Rv early log phase #1.3

source_name: H37Ra early log phase #1.3


title: H37Ra vs H37Rv early log phase #1.6

description: color swap (+) polarity

source_name: H37Ra early log phase #1.6

tag: biological sample 1, technical replicate 6

source_name: H37Rv early log phase #1.6


title: H37Ra vs H37Rv early log phase #2.4

description: color swap (+) polarity

source_name: H37Ra early log phase #2.4

source_name: H37Rv early log phase #2.4


title: H37Ra vs H37Rv early log phase #1.4

description: color swap (+) polarity

source_name: H37Ra early log phase #1.4

tag: biological sample 1, technical replicate 4

source_name: H37Rv early log phase #1.4


title: H37Rv vs H37Ra early log phase #2.3

description: color swap (-) polarity

source_name: H37Rv early log phase #2.3

source_name: H37Ra early log phase #2.3


title: H37Ra vs H37Rv early log phase #1.5

description: color swap (+) polarity

source_name: H37Ra early log phase #1.5

tag: biological sample 1, technical replicate 5

source_name: H37Rv early log phase #1.5


title: Prostate subcutaneous tumors #82 derived from human PC-3 cells, biological rep3

status: Public on Jul 02 2007

city: cambridge

first: steve

last: shen

state: MA

address: 77 mass ave

institute: MIT

description: human prostate PC3 tumors grown S.C. in nude mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on one U133A human chip and one test chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: raw data (CEL file) were normalized with RMA and further analyzied with GenePatter comparative marker selection module.

label: biotin

source_name: prostate tumors grown S.C. in nude mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (701025, Revision 3).

extract_protocol: Rneasy mini kit

tag: Genotype

value: #82 highly metastatic

tag: Age


title: H37Rv vs H37Ra early log phase #1.1

description: color swap (-) polarity

source_name: H37Rv early log phase #1.1

source_name: H37Ra early log phase #1.1


title: Prostate subcutaneous tumors #78 derived from human PC-3 cells, biological rep2

value: #78 poorly metastatic


title: Prostate subcutaneous tumors #82 derived from human PC-3 cells, biological rep2

value: #82 poorly metastatic


title: Prostate subcutaneous tumors #78 derived from human PC-3 cells, biological rep1


title: Sepsis patient (sample V9)

status: Public on Jul 01 2007

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

country: Australia

institute: Nepean Hospital

description: This sample is included in the validation set

hyb_protocol: SuperScript™ Plus Indirect cDNA Labeling System for DNA Microarrays (Invitrogen)

scan_protocol: GenePix 4000B laser scanner and GenePix software(Axon Instruments)

data_processing: Background subtraction followed by Lowess print-tip group Normalization, include genes which have (1). at least 80% of expression data with 2 fold change in either direction from the gene's median value, (2) at least 50% of expression data non-missing

source_name: Neutrophil

extract_protocol: RiboPure-Blood kit (Ambion)

tag: Sepsis Patient

source_name: Cell line

tag: Universal Reference RNA


title: Control patient (sample V6)

description: This sample is included in the validation group

scan_protocol: GenePix 4000B laser scanner and GenePix software (Axon Instruments)

data_processing: Background subtraction followed by Lowess print-tip group Normalization, include genes which have 1. at least 80% of expression data with 2 fold change in either direction from the gene's median value, (2) at least 50% of expression data non-missing

label_protocol: SuperScript™ Plus Indirect cDNA Labeling System for DNA Microarrays (Invitrogen)

extract_protocol: RiboPure-Blood kit (AmbionTM)

tag: Control Patient

tag: Universal Human Reference RNA


title: Prostate subcutaneous tumors #78 derived from human PC-3 cells, biological rep3


title: Prostate subcutaneous tumors #82 derived from human PC-3 cells, biological rep1


title: Sepsis patient (sample V8)


title: Sepsis patient (sample V50)


title: Sepsis patient (sample V47)


title: Sepsis patient (sample V7)


title: Sepsis patient (sample V48)


title: Sepsis patient (sample V49)


title: H37Ra vs H37Rv log phase #1.6

description: color swap (+) polarity

source_name: H37Ra log phase #1.6

source_name: H37Rv log phase #1.6


title: PIN_11

tag: Prostatic Intraepithelial Neoplasia

source_name: Human Genomic DNA : Male

tag: Promega Normal Genomic DNA


title: Sepsis patient (sample V45)


title: Control patient (sample V5)


title: Control patient (sample V42)


title: Sepsis patient (sample V43)


title: Sepsis patient (sample V40)


title: Sepsis patient (sample V41)


title: Sepsis patient (sample V39)


title: Sepsis patient (sample V4)


title: Sepsis patient (sample V46)


title: Control patient (sample V37)


title: Sepsis patient (sample V36)


title: Control patient (sample V35)


title: Sepsis patient (sample V44)


title: Control patient (sample V38)


title: Sepsis patient (sample V34)


title: Sepsis patient (sample V33)


title: Sepsis patient (sample V3)


title: Sepsis patient (sample V29)


title: Sepsis patient (sample V32)


title: Sepsis patient (sample V20)


title: Sepsis patient (sample V31)


title: Sepsis patient (sample V23)


title: Sepsis patient (sample V22)


title: Sepsis patient (sample V28)


title: Sepsis patient (sample V2)


title: Sepsis patient (sample V21)


title: Sepsis patient (sample V25)


title: Control patient (sample V30)


title: Sepsis patient (sample V15)


title: Sepsis patient (sample V19)


title: Sepsis patient (sample V26)


title: Sepsis patient (sample V12)


title: Sepsis patient (sample V24)


title: Control patient (sample V13)


title: Control patient (sample V11)


title: Sepsis patient (sample V18)


title: Sepsis Patient (sample TP10)

description: This sample is included in the training set


title: Sepsis patient (sample V17)


title: Sepsis patient (sample V10)


title: Sepsis patient (sample V1)


title: Sepsis Patient (sample TP11)


title: Sepsis Patient (sample TP7)


title: Sepsis Patient (sample TP5)


title: Sepsis Patient (sample TP9)


title: Sepsis Patient (sample TP8)


title: Sepsis Patient (sample TP4)


title: Sepsis Patient (sample TP6)


title: Sepsis patient (sample V14)


title: Sepsis Patient (sample TP3)


title: Sepsis patient (sample V16)


title: Sepsis Patient (sample TN4)


title: Sepsis Patient (sample TP1)


title: Sepsis Patient (sample TN9)


title: Sepsis Patient (sample TN12)


title: Sepsis Patient (sample TN5)


title: Sepsis Patient (sample TN11)


title: Sepsis Patient (sample TN6)


title: Sepsis Patient (sample TN8)


title: Sepsis Patient (sample TN3)


title: Sepsis Patient (sample TM7)


title: Sepsis Patient (sample TM8)


title: Sepsis Patient (sample TN1)


title: Sepsis Patient (sample TN7)


title: Sepsis Patient (sample TP2)


title: Sepsis Patient (sample TM5)


title: Sepsis Patient (sample TN10)


title: Sepsis Patient (sample TM6)


title: Sepsis Patient (sample TM3)


title: Sepsis Patient (sample TM4)


title: Sepsis Patient (sample TN2)


title: Control Patient (sample TC10)


title: Control Patient (sample TC9)


title: Sepsis Patient (sample TM1)


title: Sepsis Patient (sample TM2)


title: Control Patient (sample TC13)


title: Control Patient (sample TC11)


title: Control Patient (sample TC6)


title: Control Patient (sample TC8)


title: Mouse Notch1 null 1

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

description: mouse with homozygous Notch1 alleles

hyb_protocol: Hybridization was carried out according to Affymetrix protocol.

scan_protocol: Scans were carried out according to Affymetrix protocol.

data_processing: RMA normalization implemented in GeneSpring GX 7.3

source_name: mouse Notch1tm1Con/tm1Con 9.5 dpc whole embryo 1

label_protocol: Microarray target was prepared following the Affymetrix protocol.  In brief, cDNA was synthesized from total RNA using the SuperScript II double-stranded cDNA synthesis kit (Invitrogen), followed by in vitro transcription, where labeled cRNA was generated (Enzo).

extract_protocol: Total RNA was isolated from whole embryos using the RNAqueous kit (Ambion), according to manufacturer's protocol.

tag: Tissue

value: mouse C57BL/6J-Notch1tm1Con/tm1Con whole 9.5 dpc embryo


title: Control Patient (sample TC7)


title: Control Patient (sample TC2)

description: This sample is included in the training group


title: Mouse Dll3 het 2

description: mouse with heterzygous D113 and wildtype alleles

source_name: Mouse Dll3neo/+ whole 9.5 dpc embryo 2

value: Mouse Dll3neo/+ whole 9.5 dpc embryo


title: Mouse Dll3 null 1

description: mouse with homozygous D113 null alleles

source_name: Mouse Dll3neo/neo whole 9.5 dpc embryo 1

value: Mouse Dll3neo/neo whole 9.5 dpc embryo


title: Mouse wild type 1

description: mouse with wildtype alleles at both loci

source_name: Mouse +/+ whole 9.5 embryo 1

value: Mouse +/+ whole 9.5 embryo


title: Control Patient (sample TC3)

description: This sample is included in the training set.


title: Control Patient (sample TC4)


title: Mouse Notch1 null 2

description: mouse with homozygous Notch1 alleles

source_name: Mouse Notch1tm1Con/tm1Con whole 9.5 dpc embryo 2


title: 200:NIH SCFA replicate 2

status: Public on Jun 30 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Trophozoites after long term axenic growth. Isolated mid-log phase

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: Trophozoites grown in LG + Short chain fatty acids

label_protocol: Affymetrix single amplification

tag: Strain

tag: Media

value: LG + short chain fatty acids

tag: Long term axenic growth


title: Mouse Notch1 het 1

description: mouse with heterzygous Notch1 and wildtype alleles

source_name: Mouse Notch1tm1Con/+ whole 9.5 dpc embryo 1


title: Control Patient (sample TC1)


title: Control Patient (sample TC5)


title: 200:NIH replicate 2

source_name: Trophozoites grown in TYI

value: TYI


title: 200:NIH TSA replicate 2

source_name: Trophozoites grown in LG + 300 nM Trichostatin A

value: LG + 300 nM TSA


title: Mouse wild type 2

source_name: Mouse +/+ 9.5 dpc whole embryo 2

value: Mouse +/+ 9.5 dpc whole embryo 2


title: 200:NIH SCFA replicate 1


title: 200:NIH TSA replicate 1

source_name: Trophozoites grown in LG + 150 nM Trichostatin A

value: LG + 150 nM TSA


title: Mouse Dll3 null 2

description: mouse with homozygous D113 null alleles

source_name: Mouse Dll3neo/neo whole 9.5 dpc embryo 2


title: 200:NIH TSA replicate 3

source_name: Trophozoites grown in LG + Trichostatin A for 72 hours


title: Embryo heart at E13.5, KO-4

city: Los Angeles

first: Weiguang

last: Zhong

address: 675 Charles Young Drive

department: Cardiology

institute: UCLA

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Total RNA (100 ng) was hybridized to the Sentrix® MouseRef-8 Expression BeadChip (Illumina, Inc. San Diego, CA) that contains probes for ~20,000 transcripts

data_processing: The data were analyzed with Illumina Inc. BeadStudio version 1.5.0.34 and normalized by rank invariant method.

label: Biotin Streptavidin-Cy3

source_name: KO Mouse embryo hearts between E12.5-15.5

label_protocol: Biotinylated cRNA were synthesized by the Ambion total prep RNA amplification kit. cDNA was quantified and normalized to 77 ng/mcL

extract_protocol: Cardiac myocyte RNA was isolated using TRIZOL®Reagent (Sigma).  RNA quality was assessed using an Agilent 2100 bioanalyzer.

treatment_protocol: Embryos and tissues were taken from various stages under the dissecting scope. Selected hearts were rinsed with ice cool PBS and placed in the Trizol solution (GibcoBRL).

value: wildtype vs Myc-null

tag: Cardiac myocyte proliferation and apoptosis comparison, effect of wildtype vs Myc-null hearts


title: 200:NIH SCFA replicate 3

source_name: Trophozoites grown in LG +Short chain fatty acids

value: LG + Short chain fatty acids


title: Control patient (sample V27)

source_name: Neutrophil

source_name: Cell line


title: Mouse Dll3 het 1

source_name: Mouse Dll3neo/+ whole 9.5 dpc embryo 1


title: Control Patient (sample TC12)


title: Embryo heart at E13.5, KO-3


title: Embryo heart at E13.5, KO-2


title: Embryo heart at E13.5, KO-1


title: Antimycin A treatment in HT1080

status: Public on Jun 29 2007

city: Seoul

first: Hye Jin

last: Jung

address: 134 Shinchon-dong,Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

hyb_protocol: Hybridization - the DNA chip was hybridized with a mixture of fluorescently labeled cDNAs from control and treated cells at 58 °C for 16 hr

scan_protocol: Scan Protocol - the DNA chip was scanned using ScanArray Lite (Perkin-Elmer Life Sciences, Billerica, MA).

data_processing:
Data processing
- The raw data was normalized by LOWESS normalization method.

source_name: HT1080 human fibrosarcoma cell line

label_protocol: Fluorescently labeled cDNA for cDNA microarray analysis was prepared by the reverse transcription of total RNA in the presence of aminoallyl-dUTP followed by coupling of the Cy3 dye

extract_protocol: Total RNA was extracted using TriZol and then cleaned using QIAGEN RNeasy mini kit.

tag: For Ch1, RNA was prepared from untreated HT1080 cells.

source_name: HT1080 human fibrosarcoma cell line treated with 10microM antimycin A

label_protocol: Fluorescently labeled cDNA for cDNA microarray analysis was prepared by the reverse transcription of total RNA in the presence of aminoallyl-dUTP followed by coupling of the Cy5 dye

tag: For Ch2, RNA was prepared from HT1080 cells treated with 10micromolar antimycin A for 24 hours.


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Biological Replicate1)

first: Susan

middle: L

last: Ettinger

address: 2660 Oak Street

department: Urologic Sciences

institute: Faculty of Medicine

hyb_protocol: 3DNA array detection 350 kit (Genisphere, Hatfield, PA)

scan_protocol: Two fluorescent images (Cy3 and cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life and Analytical Sciences, Inc., Wellesley, MA)

data_processing: Arrays were scanned at excitation wavelengths of 532 and 632 nm to detect Cy3 and Cy5 respectively. Signal quality and quantity were assessed using Imagene 5.6 (Biodiscovery, San Diego, CA).Signal median from Imagene were analyzed in GeneSpring 6.1 (Silicon Genetics, Redwood City, CA)

source_name: Docetaxel (Biol rep 1)

label_protocol: 10ug of total RNA was used to generate Cy3-labeled 3DNA DNA Dendrimer (Genisphere, Hatfield, PA) probes according to the manufacturer’s (Genisphere, Hatfield, PA) directions and hybridized to 70-mer oligonucleotide arrays.

extract_protocol: Total RNA was isolated using the Trizol method (Invitrogen) according to manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada) and RNA 6000 nano kit (Agilent). RNA was quantitated using the Nanodrop ND-1000 Spectrophotometer, Nanodrop Technologies, Wilmington, DE

treatment_protocol: LNCaP cells were treated with Docetaxel(3.0nM) for 72h

tag: LNCaP prostate cancer cells

source_name: Vehicle control (<0.0001% DMSO)

label_protocol: 10ug of total RNA was used to generate Cy5-labeled 3DNA DNA Dendrimer (Genisphere, Hatfield, PA) probes according to the manufacturer’s (Genisphere, Hatfield, PA) directions and hybridized to 70-mer oligonucleotide arrays.

treatment_protocol: LNCaP cells were treated with vehicle control (<0.0001% DMSO) for 72h


title: Embryo heart at E13.5, WT-2

source_name: WT Mouse embryo hearts between E12.5-15.5


title: siQPC treatment in HT1080

tag: For Ch1, RNA was prepared from untreated HT1080 cells

source_name: HT1080 human fibrosarcoma cell line treated with 200nanoM siQPC

tag: For Ch2, RNA was prepared from HT1080 cells treated with 200nanomolar siQPC for 24 hours


title: HTI-286 in docetaxel-refractory prostate cancer (Dye flip2)

source_name: HTI-286 (Dye flip2)

treatment_protocol: LNCaP cells were treated with HTI-286 (0.75nM) for 72h


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Biological Replicate2)

hyb_protocol: 3DNA array detection 350 kit (Genisphere, Hatfield, PA

source_name: Docetaxel (Biol rep2)


title: Embryo heart at E13.5, WT-3

tag: Genotype


title: intestine_PPARa-knockout_treated_rep3

status: Public on Jun 28 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: small intestine PPARalpha knockout mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w.

data_processing: GCRMA version 2.20, emperical Bayes

value: 129Sv (PPARalpha knockout)

tag: Gender

value: male

tag: Age

value: 14 weeks

value: small intestine


title: intestine_wildtype_treated_rep3

description: small intestine wild type mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w.

value: 129Sv (wildtype)


title: HTI-286 in docetaxel-refractory prostate cancer (Biological Replicate 3)

source_name: HTI-286 (Biological replicate 3)


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Dye flip1)

source_name: Docetaxel (Dye flip1)


title: intestine_wildtype_treated_rep2


title: HTI-286 in docetaxel-refractory prostate cancer Biological Replicate 2

source_name: HTI-286 (Biological replicate 2)


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Dye flip3)

source_name: Docetaxel (Dye flip3)


title: HTI-286 in docetaxel-refractory prostate cancer (dyeflip3)

source_name: HTI-286 (Dye flip3)


title: intestine_PPARa-knockout_treated_rep2


title: intestine_wildtype_treated_rep1


title: intestine_PPARa-knockout_treated_rep1


title: HTI-286 in docetaxel-refractory prostate cancer (Biological Replicate 1)

data_processing: Arrays were scanned at excitation wavelengths of 532 and 632 nm to detect Cy3 and Cy5 respectively.  Signal quality and quantity were assessed using Imagene 5.6 (Biodiscovery, San Diego, CA).Signal median from Imagene were analyzed in GeneSpring 6.1 (Silicon Genetics, Redwood City, CA)

source_name: HTI-286 (Biological replicate 1)

extract_protocol: Total RNA was isolated using the Trizol method (Invitrogen) according to manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada) and RNA  6000 nano kit (Agilent). RNA was quantitated using the Nanodrop ND-1000 Spectrophotometer, Nanodrop Technologies, Wilmington, DE

treatment_protocol: LNCaP cells were treated with  HTI-286 (0.75nM) for 72h

treatment_protocol: LNCaP cells were treated with  vehicle control (<0.0001% DMSO) for 72h


title: HTI-286 in docetaxel-refractory prostate cancer (Dye Flip 1)

source_name: HTI-286 (Dye Flip 1)


title: Embryo heart at E13.5, WT-1


title: SRF Mut. IgM+IgD+ (GBF0611)

status: Public on Jun 27 2007

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: SRF Mut. IgM+IgD+ cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: FACS sorted IgM+IgD+ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: primary cells

extract_protocol: Rneasy

tag: genetic modification

value: Cd19-cre mediated deletion of the SRF Gene

tag: tissue

value: spleen:FACS sorted IgM+IgD+ cells


title: Ratio Differential of Normal CD34+ cells unmobilized stimulated or not by SDF1alpha

city: Villejuif

first: Le Bousse

last: Marie-Caroline

address: 14, Avenue Paul-Vaillant Couturier

institute: Inserm

description: oligomicroarray glass slide

hyb_protocol: Total RNA was used for synthesizing the oligomicroarray probes of aRNA type (Ambion, Applied Biosystems, Foster City, US); Synthesis was carried out with an Ambion amino-allyl kit by two successive amplification cycles of 8 hours each to obtain a minimum of 12μg per probe. Incorporation of NHS-cyanine Cy3 (un-stimulated control) and NHS-cyanin Cy5 (SDF-1 condition) was indirectly carried out following the amplification. Each probe was hybridized on an oligomicroarray chip from MWG (10K-Va). Slides were scanned with an Affymetrix Scanner 428, at 532 nm for Cy3 and 635 nm for Cy5. To minimize spatial bias, data were normalized on the spot mean by using the LOWESS method. The ratio -2 and +2 were kept for the differential threshold.

scan_protocol: Affymetrix scanner 428 Resolution 10 µm 532 nm Cy3 635 nm Cy5 Software : Jaguard Affymetrix

data_processing: normalization on the mean intensity of the microarray by Affymetrix software Jaguard, after subtraction of one background, and in last LOWESS normalization by MIDAS freeware of TIGR institute. (www.tigr.org)

source_name: Normal CD34+ cells unmobilized control not stimulated

label_protocol: Probe synthesis : 2 amplification cycles Ambion of 8 hours with amino-allyl NHS-cyanine indirect incorporation

growth_protocol: serum and cytokines free stem alpha medium

extract_protocol: Trizol extraction and RNeasy clean up

treatment_protocol: not stimulated

tag: Pool of 42 normal peripheral Blood CD34+ cells unmobilized

tag: Control 16 hours of culture not stimulated

tag: cyanine 3

source_name: Normal CD34+ cells unmobilized  stimulated by SDF1alpha

treatment_protocol: SDF1 alpha 0.5 ng/ml

tag: Control 16 hours of culture stimulated by SDF1 alpha 0.5 ng/ml

tag: cyanine 5


title: R6 restriction digests : DdeI

status: Public on Jun 26 2007

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

description: Bijlsma JJ, Burghout P, Kloosterman TG, Bootsma HJ et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol 2007 Mar;73(5):1514-24. PMID: 17261526

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).

organism: Streptococcus pneumoniae R6

source_name: Streptococcus pneumoniae R6

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.3) in M17 containing 0.25% glucose (GM17). Cells were harvested by centrifugation for 1 min at 10,000 rpm at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at –80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75–150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Furter purification was done using the High Pure RNA isolation, using the suppliers protocol.

tag: Target

tag: Control


title: R6 restriction digests : AluI


title: R6 restriction digests : TaqI

tag: control


title: mES_ESF58/2

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

hyb_protocol: according to standard Agilent protocol.

scan_protocol: Agilent scanner and software

data_processing: Agilent Feature Extraction software; gProcessedSignal; processed Cy3 Signal

source_name: mouse embryonic stem cell line ESF58/1

label_protocol: Agilent labeling kit

growth_protocol: grown on irradiated MEFs in DMEM with 15% KSR, BME, NEAA, L-glutamine, & LIF

extract_protocol: TRIzol

tag: undifferentiated


title: mES_ESF175/1

source_name: mouse embryonic stem cell line ESF175/1


title: pGHost vs mariner slide 92

source_name: Streptococcus pneumoniae TIGR4/R6 mariner

tag: mariner

source_name: Streptococcus pneumoniae TIGR4/R6 pGHost

tag: pGHost


title: post-ES_EpiSC-7_P25

source_name: EpiSC line EpiSC-7 passage 25

growth_protocol: grown on irradiated MEFs in DMEM with 15% KSR, BME, NEAA, L-glutamine, & FGF2


title: pGHost vs mariner slide 87


title: post-ES_EpiSC-5

source_name: EpiSC line EpiSC-5


title: SRF Mut. IgM+IgD+ (GBF0552)

description: SRF Mut. IgM+IgD+ cells


title: post-ES_EpiSC-7_P20

source_name: EpiSC line EpiSC-7 passage 20


title: mES_ESF122

source_name: mouse embryonic stem cell line ESF122


title: hES_BG03

hyb_protocol: Illumina Whole Genome Gene Expression Rev. D

scan_protocol: BeadStation

data_processing: rank invariant normalization

source_name: human embryonic stem cell line BG03

growth_protocol: cultured on irradiated MEFs in DMEM/F12 with 20% KSR, BME, NEAA, L-glutamine, and FGF2


title: SRF Wt. IgM+IgD+ (GBF0551)

description: SRF Wt. IgM+IgD+ cells

value: no modification


title: hES_ES01

source_name: human embryonic stem cell line ES01

label_protocol: Illumina Whole Genome Gene Expression Rev. D


title: hES_H9

source_name: human embryonic stem cell line H9


title: SRF Wt. IgM+IgD+ (GBF0610)

description: SRF Wt. IgM+IgD+ cells


title: pGHost vs mariner slide 175


title: GAF zinc slide 113

hyb_protocol: Bijlsma JJ, Burghout P, Kloosterman TG, Bootsma HJ et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol 2007 Mar;73(5):1514-24. PMID: 17261526

source_name: Streptococcus pneumoniae TIGR4/R6

tag: control GM17 without zinc

tag: target GM17 + zinc


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Biological Replicate3)

city: Vancouver

source_name: Docetaxel (Biol rep3)

tag: LNCaP prostate cancer cells

source_name: Vehicle control (<0.0001% DMSO)


title: GAF zinc slide 34

scan_protocol: Bijlsma JJ, Burghout P, Kloosterman TG, Bootsma HJ et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol 2007 Mar;73(5):1514-24. PMID: 17261526

source_name: GAF GM17

source_name: GAF GM17+zinc


title: Terpestacin treatment in HT1080

source_name: HT1080 human fibrosarcoma cell line

tag: For Ch1, RNA was prepared from untreated HT1080 cells.

source_name: HT1080 human fibrosarcoma cell line treated with 20microM terpestacin

tag: For Ch2, RNA was prepared from HT1080 cells treated with 20micromolar terpestacin for 24 hours.


title: GAF zinc slide 35

data_processing: Bijlsma JJ, Burghout P, Kloosterman TG, Bootsma HJ et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol 2007 Mar;73(5):1514-24. PMID: 17261526

tag: Target GM17+zinc

tag: GM17 without zinc


title: GAF zinc slide 114

label_protocol: Bijlsma JJ, Burghout P, Kloosterman TG, Bootsma HJ et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol 2007 Mar;73(5):1514-24. PMID: 17261526

tag: Target GM17 + zinc


title: Larval Reference, biological rep 3 of set 3

status: Public on Jun 25 2007

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description: Gene expression data from all wildtype mid-L2 nematode cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were normalized using Robust Multiarray analysis (RMA) in GeneTraffic (Stratagene). RMA normalized data were subjected to Significance Analysis of Microarray (SAM, Stanford) analysis. Each dataset was obtained with a False Discovery Rate (FDR) of less than or equal to 1%.

organism: Caenorhabditis elegans

source_name: RNA obtained from all cells by performing a control IP

label_protocol: A 2-round IVT protocol (modified from the Affymetrix small-sample protocol) was used to convert starting RNA into biotinylated aRNA.

growth_protocol: For MAPCeL analysis, gravid adults expressing F25B3.3::GFP (pan-neural) were subjected to bleach/NaOH treatment to release embryos. Embryos were harvested and then treated with chitinase to degrade the eggshell. Cells were dissociated and plated on poly-L-lysine coated dishes for 24 hrs to allow differentiation. Cells were removed from the culture dish and sorted using the FACStar Plus (Becton Dickinson, San Jose, CA) that had been flushed with egg buffer. ~90% enrichment of GFP+ cells was obtained. For mRNA-tagging, a synchronized population of larvae was obtained by the following method.  Gravid adults expressing either F25B3.3::FLAG::PAB-1 (pan-neural) or unc-4::FLAG::PAB-1 (A-class) transgenes were subjected to bleach/NaOH treatment to release embryos. Embryos were harvested and allowed to hatch o/n in M9 liquid. Hatched L1 larvae were harvested and placed on plates containing food to restart development. After 22-24hr, when >80% of larvae had reached the mid-L2 stage, larvae were harvested for RNA extraction.

extract_protocol: For MAPCEL analysis, RNA was isolated from sorted cells using the micro-RNA isolation kit (Stratagene) using the recommended volumes for 1 million cells. For mRNA-tagging samples, following elution/crosslink, RNAs were isolated by TriZOL extraction and isopropanol precipitation (following manufacturer's protocol).

treatment_protocol: For mRNA-tagging samples, synchronized L2 larvae were fixed in 0.5% formaldehyde, homogenized by passing through a French press (6000 psi on minicell) and using a Dounce homogenizer, and the cell-free extract isolated after a low-speed and high-speed spin. The FLAG-PAB bound RNA was isolated by immunoprecipitating with anti-FLAG antibodies, reversing the crosslink in a Tris buffer at 65 degrees Celcius, and TriZOL extracted.

tag: Wildtype (N2 isolate) nematodes


title: Larval Reference, biological rep 4 of set 3


title: Larval Reference, biological rep 5 of set 3


title: Larval Reference, biological rep 2 of set 3


title: Larval Reference, biological rep 5 of set 2


title: Larval A-class, biological rep 3 of set 3

description: Gene expression data from wildtype mid-L2 nematode A-class neuron

source_name: RNA obtained from A-class neurons after co-IP from unc-4::3XFLAG::PAB-1 transgenic

tag: unc-4::3XFLAG::PAB-1 transgenic


title: Larval Pan-neural, biological rep 3 of set 2

description: Gene expression data from all wildtype mid-L2 nematode neurons

source_name: RNA obtained from all neurons after co-IP from F25B3.3::FLAG::PAB-1 transgenic

tag: F25B3.3::FLAG::PAB-1 transgenic


title: 99-007-03_DS7136_wga F

status: Public on Jun 23 2007

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: DnaseI enriched

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.

source_name: HESC G.Stam; DnaseI enriched

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: HESC G.Stam


title: Larval Reference, biological rep 2 of set 1


title: Larval Reference, biological rep 3 of set 1


title: HTI-286 in docetaxel-refractory prostate cancer_docet (Dye flip2)

source_name: Docetaxel (Dye flip2)


title: Larval A-class, biological rep 1 of set 3


title: Larval A-class, biological rep 2 of set 3


title: E_099_086_04_DS6883_W F

description: DnaseI enriched

source_name: HCD4 Wilson; DnaseI enriched

tag: HCD4 Wilson


title: E_098_048_02_DS7213_W F

description: DnaseI enriched

source_name: HL60 ATCC; DnaseI enriched

tag: HL60 ATCC


title: Larval Reference, biological rep 4 of set 2


title: 99-007-02_DS7135_wga F

description: DnaseI enriched


title: Larval A-class, biological rep 4 of set 3


title: Larval Pan-neural, biological rep 1 of set 2


title: E_098_048_04_DS7229_W F

description: DnaseI enriched

source_name: HepG2 ATCC; DnaseI enriched

tag: HepG2 ATCC


title: Embryonic Pan-neural, biological rep 2 of set 1

description: Gene expression data from all wildtype embryonic neurons

source_name: F25B3.3::GFP positive cells (pan-neural)

tag: cultured embryonic cells from F25B3.3::GFP transgenic animals


title: Embryonic Reference, biological rep 4 of set 1

description: Gene expression data from all wildtype embryonic nematode cells

source_name: All living C. elegans sorted cells

tag: cultured embryonic cells from wildtype (N2 isolate) nematodes


title: Larval Pan-neural, biological rep 2 of set 2


title: Larval Reference, biological rep 1 of set 1


title: Larval Reference, biological rep 1 of set 3


title: Embryonic Pan-neural, biological rep 3 of set 1


title: Embryonic Reference, biological rep 1 of set 1


title: Embryonic Reference, biological rep 3 of set 1


title: Embryonic Pan-neural, biological rep 1 of set 1


title: 99-048-05_DS7147_gp_5ug F

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug F

description: DnaseI enriched


title: Embryonic Reference, biological rep 2 of set 1


title: E_099_077_04_DS7273_W F

description: DnaseI enriched

source_name: SKMC Cambrex; DnaseI enriched

tag: SKMC Cambrex


title: E_099_077_03_DS7168_W F

description: DnaseI enriched

source_name: K562 ATCC; DnaseI enriched

tag: K562 ATCC


title: 098-32-01_DS6998_WGA F

description: DnaseI enriched

source_name: CACO2 ATCC; DnaseI enriched

tag: CACO2 ATCC


title: 99-032-10_DS7190_WGA_4ug F

description: DnaseI enriched


title: pGHost vs mariner slide 117

source_name: Streptococcus pneumoniae TIGR4/R6 mariner

tag: mariner

source_name: Streptococcus pneumoniae TIGR4/R6 pGHost

tag: pGHost


title: Sample 3

type: mixed

city: Boston

first: Arjun

middle: Kumar

last: Manrai

address: 44 Binney Street, Mail Stop LW225

department: Department of Biostatistics and Computational Biology

institute: Dana Farber Cancer Institute

description: Raw and processed data

hyb_protocol: Performed by NimbleGen Systems Inc.

scan_protocol: Performed by NimbleGen Systems Inc.

data_processing: Cy5/Cy3 ratios normalized with MA2C

source_name: Human genomic DNA

label_protocol: Random primer labeling

extract_protocol: (genomic DNA extraction)

tag: Human genomic DNA

molecule: other

source_name: Spike A

extract_protocol: (spiked sample extraction)

tag: Spike A DNA


title: 098-32-03_DS7034_WGA F

description: DnaseI enriched


title: E_099_077_15_DS6897_W F

description: DnaseI enriched

source_name: HTH2 Wilson; DnaseI enriched

tag: HTH2 Wilson


title: Sample 1

description: Raw and processed data

tag: Spike A


title: C_094_75_04_PDS277_D F

description: Control genomic dna (untreated)

source_name: K562 ATCC; Control genomic dna (untreated)

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K