title: Agilent Technologies Human Genome CNV microarray set G4423B (AMADID 018897)

status: Public on Jul 31 2008

city: Santa Clara

first: Peter

last: Tsang

state: CA

address: 5301 Stevens Creek Blvd.

department: Agilent Labs

country: USA

institute: Agilent Technologies

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number. NCBI build 36, hg18

distribution: custom-commercial

first: Heidi

last: Whitby

first: Anya

last: Tsalenko

first: Emily

last: Aston

first: Sheri

last: Mitchell

first: Pinar

last: Bayrak-Toydemir

first: Christopher

middle: M

last: Hopkins

first: Garrick

last: Peters

first: Dione

middle: K

last: Bailey

first: Laurakay

last: Bruhn

first: Arthur

middle: R

last: Brothman

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


title: SHDZ

status: Public on Mar 08 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Print_530

status: Public on Jul 29 2008

first: Stuart

last: Kim

department: Department of Developmental Biology

institute: Stanford University Medical Center

organism: Caenorhabditis elegans

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine


title: RIKEN-LNCD-GSL_Mouse_16k_1.0

city: Wako

first: Charles

last: Plessy

state: Saitama

address: 2-1 Hirosawa

department: DRI

country: Japan

institute: RIKEN

organism: Mus musculus

description: This platform was prepared jointly by the Laboratory for Neuronal Circuit Development (LNCD), RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan, and the Genome Science Laboratory (GSL), Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.

first: Michela

last: Fagiolini

first: Kazunori

last: Waki

first: Takao

last: Hensch

first: Piero

last: Carninci

manufacture_protocol:
cDNA clones were rearrayed with a Q-bot instrument (Genetix) from 20 % glycerol/LB ampicillin stocks that were kept at -80 °C. A growth check was performed on all glycerol stocks. For the growth check 384-well plates were translated into four 96-well plates per 384-well plate and one bacterial culture per glycerol stock was inoculated. All plates were analyzed after 18 h of growth at 37 °C by visual inspection. We performed one Plasmid DNA Preparation per Glycerol Stock using a Montage Purification Kit (Millipore) and our robotic systems. One quality control was performed on three clones per plate, and the yield was 2.66 µg DNA ± 1.73. For the preparation of PCR templates, we diluted the plasmid DNA preparation by 1:500. 5 µl of template were amplified in 50 µl reactions in 96-well plates with 1.25 U Expand High Fidelity Taq/Tgo polymerase blend (Roche), 15 pmol of forward primer (tgtaaaacgacggccagt), 15 pmol of reverse primer (agcggataacaatttcacacagga) and 200 µM of each dNTP (TaKaRa) in 1 × Expand High Fidelity buffer (Roche). The program of the thermocycler was 2 min at 94 °C followed by 30 cycles of 15 s at 94 °C, 30 s at 60 °C, and 2 min 30 s at 68 °C, plus a final step of 7 min at 72 °C. The amplification products were then purified with Multiscreen PCR plates (Millipore) following manufacturer instruction, and dried. With this protocol, we could achieve an average yield of > 8 μg for 92.7 % of the wells.
The PCR-amplified cDNAs were resuspended in 50 % DMSO (Nacalai Tesque, Kyoto, Japan), and microarrays were printed on UltraGAPS slides (Corning) using an OmniGrid arrayer (Genomic Solutions) with Microarray Stealth Spotting pins (SMP3B, TeleChem).


title: SAGE:15:NlaIII:Triticum aestivum

status: Public on Jul 22 2008

last: GEO

organism: Triticum aestivum

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Triticum aestivum using NlaIII as an anchor enzyme.

distribution: virtual


title: Whitehead-Young-Mouse-Solexa (small RNA sequences)

status: Public on Jul 30 2008

city: Cambridge

first: Whitehead

last: Institute

state: MA

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

technology: other

description:
Solexa sequencing
Data generated at Center for Advanced Genome Technology at Whitehead Institute using Genome Analyzer manufactured by Solexa/Illumina (Sequencing by Synthesis)

manufacture_protocol: not applicable


title: Customized multiple signature arrays for breast cancer

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre

description: This custom array includes ~200 gene signatures.

first: Angie

last: Tan

first: Patrick

first: Benita


title: Nimblegen single array covering Mouse Chr11:36912182-99375819

status: Public on Jul 26 2008

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: The mouse Chr11 array is based on NCBI33 build of the mouse genome (mm5) and contains 391k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout mouse region Chr11:36912182-99375819 as described in the oligonucleotide array description files.

first: Zirong

last: Li

first: Leah

last: Barrera

first: Andrew

last: Smith

first: Michael

middle: Q

last: Zhang

first: Roland

middle: D

last: Green

manufacture_protocol: Whole genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005b).


title: Print_1356

status: Public on Jul 21 2008

last: Stanford Microarray Database

organism: Saccharomyces cerevisiae


title: SAGE:22:NlaIII:Arabidopsis thaliana

organism: Arabidopsis thaliana

description: This is a virtual platform for SAGE libraries generated for Arabidopsis thaliana using NlaIII as an anchor enzyme.


title: UMCG_6.5KBAC_ARRAY

city: Groningen

first: Mirjam

last: Boelens

address: Hanzeplein 1

country: Netherlands

institute: UMCG

description:
- Slide E from Scott-Nexterion (germany)
- Epoxysilane coated
- Printing of arrays using Biorobotics Microgrid II printer with 48 nanopins(www.matrixtechcorp.com)
- The arrays consist of 48 subgrids. Each BAC-clone is printed 4 times. Replicate spots are in same/ different subgrids.

first: Klaas

last: Kok

first: Pieter

last: van der Vlies

manufacture_protocol:
High throughput mini-BAC DNA isolation:
Protocol for four 96well plates:
Day1:
1. Add 500µl of LB to each well of a square well block using the multichannel stepper pipet.
2. Inoculate 1µl of the glycerolstock  to each well and seal with a Breathseal Sheet
3. Shake at 37°C for 8h with 350rpm
4. Add 1000µl LB to a new 96 well block and inoculate 5µl of the starter culture and seal with a Breathseal Sheet
5. Shake at 37°C for 18h with 350rpm.
Day2:
6. Centrifuge for 7min at 3200 rcf
7. Remove supernatant by inverting the square well blocks above a waste container and remove remaining liquid on a paper towel.
8. Check the presence and absence of bacterial pellets. Use a internal control for a contamination check.
9. Add 30µl GTE, and carefully resuspend the pellet by pipetting 20 times up and down with a multichannel pipette and transfer the liquid into a new non skirted 96 well Microplate.
10. Add 60µl freshly prepared 0,2M NaOH, 1%SDS to each well of plate one.
11. Immediately after finishing one plate, seal it with a Micro-Amp Clear Seal and invert it very, very smoothly for two times.
12. Start to countdown 4min30sec when having inverted the first plate.
13. After 3min and 15sec centrifuge plate1 and 2 in order to spin down the liquid in the centrifuge (2000rpm for one second)
14. After 4min 30 sec start to add 50µl 7,5M Ammoniumacetate to each well of plate one, seal the plate again with a new Micro-Amp Clear Seal and carefully (!) invert the plate immediately after pipetting and put it on ice.
15. Start with the other microplates and repeat from step 11.
16. After finishing the last plate, incubate for 10 minutes on ice. Invert the plates smoothly after 3 minutes of incubating.
17. After 10min centrifuge all plates at 3200 rcf for 30 minutes at room temperature in the Beckmann Allegra centrifuge. Use the stacking tools when placing the microplates in the centrifuge.
18. Place a new 96-wells PCR plate in a rack, mount it on top of the each centrifuged old ones (A1 on A12) and quickly invert it.
19. Centrifuge again for 30min 3200rcf at room temperature.
20. Invert a second time as described at step 19 on a new non skirted 96 well Microplate.
21. Add 70µl isopropanol to each well, seal it with a tape pad and invert it very smoothly for three times.
22. Centrifuge again for 30min at 3200rcf and invert in order to remove supernatant (now the DNA is in the pellet).
23. Add 50µl 70% ethanol and seal it with a Micro-Amp Clear Seal as above
24. Centrifuge at 6000 rcf for 10min at room temperature
25. Invert to remove supernatant, beat several times against a clean tissue in order to completely remove the residual ethanol. Leave the plates inverted on a fresh tissue
26. Add 25µl MilliQ-water to each well, seal with an Adhesive PCR Foil Seal and put them in the refrigerator overnight to solve the DNA.
Day 3
Exonuclease Treatment:
27. Resuspend Exonuclease in 225µl solvent according to the manual of the Large-construct kit.
28. Add to each well 5µl of the following mix: 3µl NEB1, 0,6µl Exonuclease, 0,9µl ATP, 0,15µl RNase and 0,35µl H2O and mix carefully by smoothly pipetting five times up and down.
29. Incubate the plates at 37°C for 4-12h in a PCR machine.
30. Inactivate the exonuclease by heating up the reaction to 75°C for 10min.
Random amplification of BAC-DNA (DOP-PCR)
•Perform for each BAC/PAC-sample three Hot Start PCR reactions according this pipetting schedule:
Mix A					1 reaction:
10x reactionbuffer				3.5 μl
MgCl2					2.0 μl
dNTP's	 (4x25mM)			0.32 μl
DOP primer (100 pmol/l)			0.8 μl
BAC/PAC-DNA				1 μl
Milli Q water				27,4 μl
					----------+
					35 μl
Mix B
10x reactionbuffer				0.5 μl
Taq-polymerase				0.5 μl
Milli Q water				4 μl
					----------+
					5 μl
•Add Mix B to Mix A during the initial denaturation step of the PCR. The PCR is performed in a AB-thermal Cycler 9700 or in a 96wells MJ-Cycler using this program:
94°C	3 min.
94°C	1.5 min.
30°C	2.5 min.	10 cycles
Ramp to 72°C at 0.1 °C per second
72°C	3 min.
94°C	1.0 min.
62°C	1.5 min.	30 cycles
72°C	2.0 min.
72°C	8.0 min.
12°C	hold
•Concentrate the PCR-products by precipitation:
-Pool the DOP1, DOP2 and DOP3 products.
-Add 1 μl of Glycogen and mix.
-Add 1 μl of 3M NaAc and 240 l ethanol.
-Spin 30 min. on 6000g in the Beckman Bench top Centrifuge.
-Wash with 100 μl 70% ethanol
-Spin for 10 min. on 6000g.
-Dry the DNA-pellet by spinning the plates upside down on 600rpm for 30s.
-Dissolve the DNA-pellet in 18 μl spotting buffer.
Alternatively it is possible to concentrate the pooled DOP-PCR products by filtrating through a MilliPore Multiscreen PCR filter plate, according to the manual supplied with the kit.
•The amplified BAC/PAC-DNA is now ready for arraying.
Array printing
1. Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to
obtain the recommended final probe concentration:
DNA Probes Final Spotting Concentration
Oligonucleotides 10 - 20 μM
PCR products 0.1 – 1 mg/ml
2. Transfer an appropriate volume of probes to a microtiter plate.
3. Set up the arrayer according to the manufacturer’s recommendations. If you were
previously using slides that were thicker than 1.0 mm, for optimal spotting you may
need to re-calibrate the distance between the slide surface and the spotting pins.
4. Print the substrates at 40-50% relative humidity at 20 to 25°C.
Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to
obtain the recommended final probe concentration:
DNA immobilization
1. Incubate printed microarray slides in humidity chamber at room temperature for 30
min (see appendix for details of how to prepare this chamber) to ensure quantitative
immobilization.
2. Proceed to washing.


title: Yeast Oligo Microarray (Agilent G4140A/G4140B)

middle: P

last: Capaldi

address: Bauer 307, 7 Divinity Ave

department: MCB

institute: Harvard University


title: Broad-Mouse-Illumina-Genome-Analyzer-ChIPSeq (2007)

status: Public on Jul 25 2008

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Illumina Genome Analyzer (1G), San Diego, CA


title: Aspen 14k Array 2.1_2007 from MTU

status: Public on Jul 24 2008

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

organism: Populus tremuloides

description:
http://aspendb.mtu.edu/nsf.phtml
The Platform data table reflects the fact that the spots were duplicated on the array.

first: Yu-Ying

last: Kao

first: Maria

last: Hernandez

first: Han-Wei

last: Lin

first: David

last: Jaroch

first: Hongying

last: Jian

first: Scott

last: Harding

first: Priya

last: Ranjan

first: Stephanie

last: Drake

first: Darren

last: Touchell

first: Heidi

last: Skoog

manufacture_protocol:
The following was provided by Michigan Tech about the aspen array design:
The aspen 7K array (2nd generation)
1. Array design: The second generation aspen 7K array contains replicate subarrays of 6,705 elements in a 4×4 grid with a spot diameter of ~150 μm and a spacing of 200 μm. These elements represent ~5,400 unique JGI Populus gene models, and include various positive and
negative controls (Lucidea Universal ScoreCard, Amersham) to monitor target labeling and hybridization efficiency, as well as many known function genes derived from our previous and ongoing research.
2. Print area: The replicate subarrays occupy an approximately 18×37 mm area on the non-barcode side.
3. Spot layout: Each grid contains 12 spike controls on the top
left corner. The first 5 are calibration controls (from
high to low concentrations), followed by 1
negative control , 3 or 5 ratio controls (different
ratio combinations between Cy3 and Cy5 targets), and another negative control ,or negativeratio-negative controls.  Each grid contains 21×21
spots, except for the last row which has variable number ofempty spots.
4. Spikes: To take advantage of the spike controls, appropriate
spike mRNA samples need to be included during target
labeling (see Section C below and Amersham manual).
However, the use of spike mRNA in hybridization is optional,
and will not affect the array analysis (e.g., using global per
chip normalization etc).
5. Clone information: A gene list can be downloaded from our website (www.aspenDB.mtu.edu).
Sequence information can be obtained by searching the GenBank or our ESTDB with the MTU clone
IDs. As is the case for other large-scale projects, there are likely errors in our array system. Due to
funding limit, we have only re-sequenced a number of randomly selected array-ESTs. Other potential
errors include mis-annotation, or mis-classification with regard to the functional groups. Therefore,
additional confirmation for array-selected candidate genes will be necessary.
References: Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta 219: 694-704.


title: Synechocystis sp. PCC 6803 oligo array

city: St. Paul

first: Zhigang

last: Zhang

state: MN

address: 1479 Gortner Avenue, Suite 140

department: BioTechnology Institute

institute: University of Minnesota

organism: Synechocystis sp. PCC 6803

technology: spotted oligonucleotide

first: Ninad

last: Pendse

first: Arkady

last: Khodursky

manufacture_protocol:
1. The 70-nt oligomers were designed using ArrayOligoSelector [http://arrayoligosel.sourceforge.net/] and were synthesized by Invitrogen Corp. (Carlsbad, CA).
2. The oligos were resuspended in 5µl of 3×SSC in 384-well microwell plates to a final concentration of 66.7 pmol/µl and spotted onto poly-L-lysine coated microscopic glass slides using a 16-tip OmniGrid Microarray printer (GeneMachines, San Carlos, CA) as described previously (Eisen 1999).


title: Print_529

first: Stuart

last: Kim


title: UMDNJ Human SNP Array

city: Piscataway

first: Minjie

last: Luo

state: NJ

address: 675 Hoes Lane

department: Microbiology & Molecular Genetics

institute: University of Medicine and Dentistry of New Jersey

description: Totally 65 markers were included in the array.They are multi-site variants (MSV), paralogous sequence variant(PSV), SNPs in duplicons (SIDs), and SNP in unique region. Each maker were printed four times. Their RS numbers were shown in processed data. Here we listed the characteristics of each marker.

first: Hui

middle: Y

last: Wang

first: Xiangfeng

last: Cui

first: Honghua

last: Li

manufacture_protocol:
1.preparation of microarray slides: Pre-cleaned Gold Seal Micro slides (Becton Dickinson) were soaked in 30% bleach with shaking for 1–2 hrs followed by rinsing five times with deionized H2O and three times with MilliQ H2O. Slides were then sonicated in 15% Fisher brand Versa-Clean Liquid Concentrate with heat on for 1–2 hrs followed by rinsing with shaking 10 times in deionized H2O and five times in MilliQ H2O. Slides were dried by centrifugation at 1,000 rpm for 5 min with a slide holder in a GS-6 Beckman centrifuge, and then were baked at 140°C in a vacuum oven for 4–5 hrs (Fisher Scientific Model 280A);
2.Each oligonucleotide probe was mixed with the Microarray Printing Solution (GenScript, Piscataway NJ) at a 1:5 ratio (v/v) to a final concentration of 50 μM in a well of a 384-well plate.
3.Probes were then arrayed onto the washed glass slides with humidity between 50% and 55%, and temperature between 24.5°C to 26.5°C.


title: Flibotte human 380k oligotest

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

description: build hg36 (hg18)

first: Donald

middle: G

last: Moerman

manufacture_protocol: see NimbleGen's website


title: Sulfolobus 3.4K long oligo array version 2.0

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

organism: Saccharolobus solfataricus P2

distribution: commercial

first: Jasper

last: Walther

first: Stan

last: Brouns

first: Harmen

last: vandeWerken

manufacture_protocol: Oligo probes were designed by Walther, Brouns and van de Werken based on the published genenomes.  Oligos were synthesized and cleaned up using an automated process and spotted on to slides.  Ocimum Biosolutions produced the slides using their established protocols.


title: Cardiff NIA 15K set, print format 2

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

description: Slides contain 16128 spots, printed in 12x4 mini grids, each with 16 rows and 21 columns. Spots representing NIA ESTs have the NIA clone number corresponding to their grid location. Some spaces on each grid are empty or blank.  Landmarks were used to align the grids, Scorecard/UT1/Rich spots are for use with a spike control. Spots actually marked as "empty" were printed with water/DMSO.

manufacturer: Cardiff University Array Facility and Wales GenePark

first: Susan

last: Hunter

first: Steven

last: Turner

first: Victoria

last: Workman

middle: C

first: Martin

middle: J

last: Evans

manufacture_protocol: Bacterial cells were grown in 96 well plates, pelleted at 2500rpm for 10 minutes, and resuspended in 50ul water. Cells were ruptured by incubation at 95 degrees celsius for 10 minutes, then spun for debris removal at 2500rpm for 10 minutes at 4 degrees. 10ul cell lysate was then added to 10ul 2xPCR mix (0.4ul 1omm dNTPs, 2ul each fwd and revs M13 primers (10pmol/ul, 2ul 10X Taq buffer, 2ul 25mM MgCl2, 0.4ul Taq polymerase (Promega), and 1.2ul sterile water) in a 96 well plate Amplification was carried out using an MWG thermocycler, 95oC, 1min then (95oC 1min, 58oC, 1min, 72oC, 30 secs). PCR products were then purified using Sephacryl S-300 and a 96 well filter plate (350ul/well). PCR products were assessed for successful amplification via 1.5% agarose gel electrophoresis. PCR products were then transferred to 384 well plates in known order then diluted to 50% original concentration with DMSO. PCR DNA samples were then used for printing on Corning CMT-GAPS slides.


title: Nimblegen custom chromosome X tiling array

city: New Haven

first: Annette

last: Molinaro

state: CT

address: 60 College St

institute: Yale University

manufacture_protocol: Spotted array with 60nt long probes tiled along the Human chrX. The probes have been tiled each 110 bp in average.


title: C. acetobutylicum ATCC824 22K Transcriptional array v2

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

organism: Clostridium acetobutylicum ATCC 824

description:
C. acetobutylicum ATCC824 Transcriptional array v2 includes over 20K 60-mer oligonucleotide probes selected after experimental testing of our proof-of-concept platforms GPL4029 and GPL4030.
The programs Comm_Oligo (Li, He et al. 2005), ROSO (Reymond, Charles et al. 2004), YODA (Nordberg 2005), ArrayOligoSelector (Bozdech, Zhu et al. 2003), OligoWiz 2.0 (Wernersson and Nielsen 2005) and Picky (Chou, Hsia et al. 2004) were used to generate several 60-mers for each Clostridium acetobutylicum ATCC824 chromosome and pSOL1 megaplasmid ORF (Nölling, Breton et al. 2001). Whenever possible the DNA sequences belonging ribosomal RNAs, tRNA and the intergenic regions of the whole genome were used as a negative set (i.e. no match allowed). A maximum identity of 75-85% to any other sequence and other parameters were set to the program defaults. On average, 32 60-mers per ORF where generated.Melting temperatures and DeltaG values for the generated oligomer and its complementary sequence were re-calculated using Hybrid 2.5 (Markham and Zuker 2005) (included in (Rouillard, Zuker et al. 2003)).
For each 60-mer, the best four non-specific matches against the Clostridium acetobutylicum ATCC 824 genome were determined using FASTA (Pearson and Lipman 1988; Pearson 1990). The melting temperatures of the heterodimers formed by a 60-mer and the complementary sequence of each of its non-specific matches were also calculated. The difference between the melting temperature between the 60-mer and each one of the heterodimers was calculated and the minimal value of the differences was recorded. The 60-mers targeting each particular ORF were ranked (in descending order) according to the minimal DeltaT previously recorded.
mRNAs from wild type and M5 C. acetobutylicum strain cultures in exponential phase where hybridized onto two pairs of slides on a dye-swap configuration using Agilent and cDNA arrays for a total of twelve arrays. After background subtraction, the intensities of the probes on each channel were ranked independently and scaled to a maximum value of 100 on each slide. For each gene four median ranks were calculated: two corresponding to the WT values (one for its probes in our previous cDNA platform GPL3820 and another for its probes in our proof-of-concept platforms GPL4029 and GPL4030) and the other two for the M5 values using the same procedure.
To select the most representative pair of probes for each gene, first we selected the probe with a mean WT rank closest to the median rank of the Agilent probes for that gene. The same procedure was applied for the M5 ranks. If the selected probe for the WT and M5 samples is the same, then we selected the second closest probe to the median rank of the strain (WT or M5) with the higher median rank on the spotted arrays (WT or M5). We did so to avoid choosing probes with very low intensities in those cases where the mRNA is not expressed by one of the strains.
Control features are automatically included on the array by Agilent and follow their naming convention. The name for our custom 60-mers is composed of the ORF name (CACXXXX or CAPXXXX), the 60-mer number (1,2 or 3), a character (d,e or f) indicating if it is the first (d), second (e) or third (f) occurrence of this specific 60-mer on this platform, and a two letter code (Ch, Co or Tr). A Ch 60-mer is a 60-mer located in the lower 50% or 500 bp (whichever is shorter) of the target ORF and has a rank of four (4) or greater. A Co 60-mer is a 60-mer located in the lower 50% or 500 bp (whichever is shorter) of the target ORF and has a rank of four (4) or smaller.  A Tr 60-mer is any 60-mer that does not meet the requirements of a Ch or Co 60-mer regarding location and/or rank.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

first: C

last: Paredes

first: E

middle: T

manufacture_protocol: See manufacturer's web site


title: FHCRC Yeast Amplicon v1.1

status: Public on Mar 18 2005

city: Seattle

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: Yeast ORF microarrays were constructed employing a set of 6229 ORF-specific PCR primer pairs (Research Genetics, Huntsville, AL). Individual PCR products were verified as unique via gel electrophoresis, purified, and mechanically "spotted" onto glass microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines, San Carlo, CA).


title: Ramaciotti centre-miRNA-1488-v8.1

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: For 2 colour spotted array labelling. 4X4 grip array formation. Duplicates next to each other. Repeated 4X4 on the next grid.

first: RubyCY

first: Zi-Hui

last: Lo

first: Ian

middle: W

last: Dawes

manufacture_protocol:
Element generation protocol: amino-modified oligonucleotide with individual monomers substituted with LNA (Locked Nucleic Acid)
Element type: Exiqon miRCURY LNA capture probes
Production protocol: contact pin (Biorad Chipwriter) in 48 pin formation


title: Print_1126

status: Public on Jul 18 2008

first: Kevin

last: Kwei

address: 269 Campus Dr.

institute: Stanford


title: Scerevisiae_tlg Array

status: Public on Jul 19 2008

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

description: The platform contains 25 nucleotide probes spaced every 8 bp covering one strand of the whole /Saccharomyces cerevisiae/ genome sequence and a second set of probes offset 4 bp from the first set to cover the other strand.  Lee et al. (2007) Nature Genetics 39: 1235-1244.

manufacture_protocol: see manufacturer's web site


title: Agilent Technologies Human Genome CNV microarray set G4423B (AMADID 018898)

city: Santa Clara

first: Peter

last: Tsang

address: 5301 Stevens Creek Blvd.

institute: Agilent Technologies

first: Heidi

last: Whitby

first: Anya

last: Tsalenko

first: Emily

last: Aston

first: Sheri

last: Mitchell

first: Pinar

last: Bayrak-Toydemir

first: Christopher

middle: M

last: Hopkins

first: Garrick

last: Peters

first: Dione

last: Bailey

first: Laurakay

last: Bruhn

first: Arthur

last: Brothman


title: Yeast ncRNA and expression array

status: Public on Jul 16 2008

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: Array incorporates the probe set previously developed for analyzing ncRNAs from yeast (PMID 15920104).  Additional probes are included for estimating mRNA expression for ~6000 genes, previously predicted snoRNAs (PMID 17577407) and ncRNAs that were excluded from the original study.

manufacture_protocol: Custom in situ DNA synthesis on glass slides.


title: Flibotte C. elegans 380k oligotest

first: Stephane

last: Flibotte

description: build CE4, WormBase v. WS170

first: Donald

last: Moerman


title: Print_501

city: Stanford

first: Stuart

last: Kim

institute: Stanford University Medical Center


title: ORNL Shewanella oneidensis 5.7k array

status: Public on Jul 17 2008

city: Oak Ridge

first: Karuna

last: Chourey

state: TN

address: 1, Bethel Valley Road

department: Chemical Sciences Divison

institute: Oak Ridge National Lab

organism: Shewanella oneidensis MR-1

manufacture_protocol: The predicted ORFs of Shewanella oneidensis MR-1 (NC_004347) are PCR amplified. The PCR amplicons are deposited onto Telechem Superamine slide (Telechem, Inc., Sunnyvale, Calif.) in duplicate. There are 32 blocks on the array. In each block, there are 18 columns and 20 rows. See detailed description on manufacture protocol in Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis (J. Bacteriol. Vol 186, No.22: 7796-7803).


title: High-throughput pyrosequencing of small RNAs in Tomato fruits and leaves

city: Norwich

first: Frank

last: Schwach

address: University of East Anglia

department: School of Computing Sciences

institute: University of East Anglia

organism: Solanum lycopersicum

description: The dataset contains Lycopersicon esculentum cv. MicroTom endogenous small RNA sequences in the range 16-30 nucleotides. High-throughput sequencing was carried out at 454 Life Sciences. Please see www.454.com for details of the technology. Total RNA was extracted from tomato leaf, bud before flower blooming and different developmental stages of whole fruits.Small RNA sequences that did not match tRNA or rRNA sequences (obtained from RFAM), The Genomic tRNA Database and EMBL were mapped to bacs version 175 of the Solanum lycopersicum cv. Heinz 1706-BG genome.  The number of matches to the unfinished genome, if any, is recorded in the table.

first: Simon

last: Moxon

first: Runchun

last: Jing

first: Gyorgy

last: Szittya

first: Rachel

middle: L

last: Rusholme Pilcher

first: Vincent

last: Moulton

first: Tamas

last: Dalmay

manufacture_protocol: see manufacturer website www.454.com


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATq306.01.Z)

city: Tucson

first: David

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

manufacturer: The Galbraith Laboratory, University of Arizona

manufacture_protocol: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATq306.01.001-ATq306.01.400 (http://www.ag.arizona.edu/microarray).


title: Eppendorf Custom Human ABC DualChip

status: Public on Jul 12 2008

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

manufacture_protocol:
The genes on the low density microarray (termed DualChip human SBCL) are presented in Table I in Gillet JP et al. CANCER RESEARCH 64, 8987–8993, December 15, 2004. This microarray contains two arrays per slide with a range of 41 transporter genes composed of 38 ABC transporters, 1 cationic transporter (IMPT), and  2 ATP-sensitive potassium channels (Kir6.1 and 6.2). The microarray is based on the Xmer technology developed by Eppendorf (Hamburg, Germany). It is composed of single strand DNA probes attached to a glass support by a covalent link. Each DNA probe is present in triplicate on the array and designed for the detection of gene expression (Figure 1).
To minimize the effect of variation sources, the microarray contains several controls which are also intended for normalization of signal intensities. This set of controls includes positive and negative hybridization controls, a positive detection concentration curve, negative detection controls, internal standards (mix of spiking RNAs), and a set of housekeeping genes. The specificity of the capture-probes has been checked in vitro and in silico. The reproducibility and the sensitivity of low density arrays (termed DualChip) were demonstrated previously:
Gillet JP, Efferth T, Steinbach D, Hamels J, de Longueville F, Bertholet V et al. Microarray-based detection of multidrug resistance in human tumor cells by expression profiling of ATP-binding cassette transporter genes. Cancer Res 2004; 64:8987-8993.
de Longueville F, Lacroix M, Barbuto AM, Bertholet V, Gallo D, Larsimont D et al. Molecular characterization of breast cancer cell lines by a low-density microarray. Int J Oncol 2005; 27:881-892.
Meneses-Lorente G, de Longueville F, Dos Santos-Mendes S, Bonnert TP, Jack A, Evrard S et al. An evaluation of a low-density DNA microarray using cytochrome P450 inducers. Chem Res Toxicol 2003; 16:1070-1077.


title: Print_1257

first: Kevin

last: Kwei

state: CA

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: SuperArray Mouse stem cell oligonucleotide array

status: Public on Jul 11 2008

city: Lund

first: Vanessa

last: Hall

address: Solvegatan 17

country: Sweden

institute: Lund University

description: Contains 263 stem cell related genes printed on nylon membrane.


title: Print_1256

city: Cambridge

first: Kate

last: Rubins

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

organism:
Homo sapiens
Monkeypox virus
Orthopoxvirus vaccinia
Variola virus


title: AURATUS: The goldfish environmental genomics project 17K array v1.1

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

institute: University of Ottawa

organism:
Carassius auratus
Cyprinus carpio

manufacturer: University of Liverpool; Laboratory for Environmental Gene Regulation (LEGR)

first: Christopher

last: Martyniuk

first: Jan

last: Mennigen

first: Susanna

last: Wiens

first: Wudu

last: Lado

first: Dapeng

last: Zhang

first: Vicki

last: Marlatt

first: Colin

last: Cameron

last: Crump

first: Emily

last: Gerrie

first: Xuhua

last: Xia

first: Andrew

middle: R

last: Cossins

first: Vance

last: Trudeau

manufacture_protocol:
see Gracey et al. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101:16970-5, 2004.  and
see Williams et al. Genomic resources and microarrays for the common carp Cyprinus carpio L. J Fish Biol 72:2095-2117, 2008.


title: yeast48canada (condensed version)

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description:
48 subarrays (spots organised in 17 rows and 16 columns per subarray)
distributed in 12 rows and 4 columns of subarrays.
Controls are 3XSSC and Arabidopsis

The Platform data table reflects a condensed representation of the array's duplicate features.
The full, uncondensed array is deposited under GPL764.

manufacturer: Microarray Centre University Health Network Toronto Medical Discovery Tower 101 College Street, Rm 9-301 Toronto, Ontario, M5G 1L7

relation: Alternative to: GPL764 (uncondensed version)

manufacture_protocol:
1. Acquisition of bacterial clone set - our Yeast 6.4k clone set is derived from Research Genetics Genepairs, Detailed information about the ORFs and sequences can be found at http://www.yeastgenome.org/
2. Clone set is PCR amplified and DNA purified in working 96 well plates.
3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from .10ug/ul to 0.25ug/ul.  These are used for spotting.
Microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Microarray Layout Specifications Grid Rows12 Grid Cols 4 Rows 17 Cols 16 Grid to Grid Distance (um) 4500 Spot to Spot Distance (um) 200


title: Print_1110

state: MA


title: Print_1046


title: Brems/Hoheisel/Clayton T. brucei genomic array (DKFZ/ZMBH, Heidelberg)

status: Public on Jul 15 2008

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

institute: CSIC

organism: Trypanosoma brucei

manufacturer: S. Brems, C. Clayton and J. Hoheisel, DKFZ & ZMBH, Heidelberg, Germany

first: Stefanie

last: Brems

first: Jörg

last: Hoheisel

first: Christine

last: Clayton

manufacture_protocol: Independent random genomic clones from T. brucei 927 were used to create PCR products which were spotted onto poly-L-lysine coated glass slides. 75% of insert sizes were within 1.8-2.5 kb. The arrays contain 24,567 spots, and would be expected to cover at least 80% of the trypanosome genome.


title: Human 1.7K Array (H1.7K)

city: Sudbury

first: Baoqing

last: Guo

address: 41 Ramsey Lake Road

department: Tumor Biology

institute: Advanced Medical Research Institute of Canada

manufacturer: The University Health Network Microarray Centre, Toronto, Canada

manufacture_protocol: microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use, Double-spotted array containing 1,718 well-characterised human ESTs. Most of the clones are associated with Swiss-Prot IDs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation.


title: Viro4

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

organism: Viruses

description: This platform includes ~15,000 oligonucleotides derived from ~1200 viral species.  The best-performing viral oligonucleotides from the Viro3 platform (GPL3429) were carried over to the Viro4 platform.  The platform also includes additional viral oligonucleotides generated using a computer algorithm to obtain desired coverage of viral taxonomic groups (ViroTax, Fischer K, manuscript in preparation).  This platform also includes the following control oligonucleotides: human endogenous retroviruses, highly expressed human genes, and yeast intergenic sequences.

first: Kael

middle: F

last: Fischer

first: Charles

last: Chiu

first: Amy

last: Kistler

first: Anatoly

last: Urisman

first: Don

last: Ganem

first: Joseph

manufacture_protocol: Spotted 70-mer nucleotides on glass


title: MPIMG-Human-Solexa sequencing-HEK and B cell RNA

status: Public on Jul 03 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

country: Germany

institute: Max Planck Institute for molecular genetics

organism: Homo sapiens

description: Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)


title: MPIMG-Human-Solexa sequencing HEK PolIIa ChIP


title: DKFZ/Operon mouse 35K Oligo Set v4.0

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

institute: DKFZ

description:
Spotted long oligonucleotide array produced using the Operon mouse Genome Oligo Set Version 4.0 (35,912 70mer oligonucleotides)
Keywords = spotted
Keywords = mouse
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon

manufacturer: Division Molecular Genetics, DKFZ Heidelberg, Germany

first: Meinhard

last: Hahn

first: Peter

last: Lichter

manufacture_protocol: 70mer oligonucleotides were diluted at 40 µM in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: OSU RIGUA (Ruminant Immuno-inflammatory Gene Universal Array)

status: Public on Jul 02 2008

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

organism: Ovis aries

description: For additional information please contact Prof. John Hopkins or S. Rhind at The University of Edinburgh

manufacturer: Edinburgh Research and Innovation, The University of Edinburgh

manufacture_protocol:
Researchers at the University of Edinburgh have constructed a microarray to allow investigation into a large set of immuno-inflammatory genes regulated in response to disease, vaccination and therapeutic interventions in ruminants. Specifically designed to investigate the host response to infection by Mycobacterium avium subsp. paratuberculosis (Johne's disease), the microarray can also be applied to other disease states in ruminants. The array will also provide information on selectable traits that may confer resistance to Johne's disease and responses to vaccination. The gene array consists of approximately 600 ruminant immuno-modulatory genes backed up by a database and management system to allow full interrogation of experimental data.
The full array, or RIGUA (Ruminant Immuno-inflammatory Gene Universal Array), consists of some 600 ruminant genes each represented by two non-overlapping 75-mer oligonucleotides. These have been selected to enable investigations into the immune response to infection and other challenges, including vaccination, in ruminants. It will therefore be useful in defining those genes involved in the development of disease, which have an immuno-inflammatory component thus contributing to animal improvement and breeding. It will also be useful in vaccine and adjuvant response studies in the development of vaccines to ruminant disease.


city: Hanover

first: Michael

last: Whitfield

state: NH

address: 7400 Remsen

department: Genetics

institute: Dartmouth Medical School

description: See Accession GPL1708 for official Agilent Whole Human Genome Oligo Microarray G4112A

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


title: National University of Singapore NimbleGen 385K Promoter Array version 1

status: Public on Jul 01 2008

city: Singapore

first: Wah Heng

last: Lee

address: 60 Biopolis Street

institute: Genome Institute of Singapore

manufacture_protocol: see NimbleGen website


title: Zebrafish 12kb promoter 244K array_slide 1 of 2

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

organism: Danio rerio

manufacture_protocol: As described at www.agilent.com


title: NimbleGen Mouse Promoter 393K Array, 2 of 2

city: Berkeley

first: Jason

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

organism: Mus musculus

manufacture_protocol: Maskless photochemistry, (MM8; NCBI Build 36; 2006-07-18_MM8_promoter_2of2)


title: Whitehead Institute Solexa sequencing

first: Whitehead

last: Institute

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

description: Sequencing was carried out using the Solexa/Illumina Genome Analyzer


title: SAGE:10:NlaIII:Dictyostelium discoideum

status: Public on Jul 09 2008

last: GEO

organism: Dictyostelium discoideum

description: This is a virtual platform for SAGE libraries generated for Dictyostelium discoideum using NlaIII as an anchor enzyme.


title: yeast48canada

status: Public on Feb 16 2004

first: Javier

last: Arroyo

organism: Saccharomyces cerevisiae

description:
48 subarrays (spots organised in 17 rows and 16 columns per subarray)
distributed in 12 rows and 4 columns of subarrays.
Controls are 3XSSC and Arabidopsis

The Platform data table reflects the full, uncondensed array showing all duplicate features.
A condensed representation of the array's duplicate features is deposited under GPL7054.

relation: Alternative to: GPL7054 (condensed version)


title: NimbleGen Mouse Promoter 393K Array, 1 of 2

manufacture_protocol: Maskless photochemistry, (MM8; NCBI Build 36; 2006-07-18_MM8_promoter_1of2)


title: AURATUS: The goldfish environmental genomics project v1.0

status: Public on May 18 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

manufacturer: University of Liverpool; Laboratory for Environmental Gene Regulation (LEGR); http://legr.liv.ac.uk/carpbase/index.htm

first: Kate

last: Crump

first: Emily

last: Gerrie

first: Suzanna

first: Ravinder

last: Sardana

first: Xuhua

last: Xia

last: Popesku

first: Vance

last: Trudeau

manufacture_protocol: see Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, and Cossins AR. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101:16970-5, 2004.


title: Rabbit_embryo_2304

city: JOUY EN JOSAS

first: Duranthon

last: Veronique

address: Domaine de Vilvert

department: Biologie du Développement et Reproduction

country: France

institute: INRA

organism: Oryctolagus cuniculus

description: 2304 features - 16 blocks (144 spots per block)

manufacturer: RGS platform of Genopole Toulouse Midi Pyrénées (http://genopole-toulouse.prd.fr/) and UR 444 Cellular Genetics INRA, chemin de Borde Rouge Auzeville, BP 52627, 31326 Castanet-Tolosan cedex, France

manufacture_protocol: as described in Institute Labs manual


title: SCKCEN Cupriavidus metallidurans CH34 Genomic Array

status: Public on Mar 16 2007

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

organism: Cupriavidus metallidurans CH34

first: Sebastien

last: Monchy

first: Mohammed

middle: A

last: Benotmane

first: Max

last: Mergeay

manufacture_protocol:
1.  Oligos are synthsized and arrayed in Greiner 96-deep well plates. Each well contains more than 10nmol of 60-mer oligo and are resuspended in water to10µM.
2. Resuspended oligos in water to 10 uM are rearrayed into 384-well (10µl transfered from 96 to 384 well plates), Genetix polystyrene V-bottom plates (cat# X6004).
5. 10µl of 2x spotting bufferis added to each well of the 384 plate, these plate are considered as spotting master plates
7. Shake plates near maximum rotational speed on flat-bed shaker for 10 minutes.
8. Centrifuge plates at 2000 rpm for 3 minutes prior to spotting.
9. Remove seals and cover with plate lids. Place in appropriate location (biobank in MicroGrid spotting robot) just before print run is started to minimize evaporation time before printing.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.


title: Broad-Mouse-Illumina-Genome-Analyzer-ChIPSeq (Meissner)

status: Public on Jul 06 2008

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Illumina Genome Analyzer (1G), San Diego, CA


title: Zebrafish 12kb promoter 244K array_slide 2 of 2

first: Fiona

last: Wardle


title: ENS SGDB Mus musculus 22k Compugen

status: Public on Jul 04 2008

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

description:
Mouse OligoLibraryTM. The Mouse OligoLibraryTM by Compugen and Sigma-Genosys combines Compugen's superior computational platform and oligo design tools with Sigma's high-quality oligo synthesis.
Oligo length: 65 bases.
Modification: 5Õ-C6 amino modifier.
Number of oligos: 21,997.
Number of genes: 21,587 (excluding controls).
Positive controls: four oligos per plate from glyceraldehyde-3-phosphate dehydrogenase (GAPDH).
Distance from the 3Õ end: 95% of the oligos are within the range of 65Ð1,072 bases from the 3Õ end. Average distance from the 3Õ end is 379 bases.
Cross-homology: 90% of the oligos contain a predicted cross-homology of less than 81.5%. Average cross-homology is 37.7%.
Longest full match stretch: in addition to cross-homology percentage, oligos are also selected with a minimal length of sequence identity in the cross-homology alignment.
GC content: 95% of the oligos contain a GC content within the range of 40%Ð60%. Average GC content is 49.9%.

manufacturer: ENS Biology Department Transcriptome Platform

first: Stephane

last: Le Crom

first: Piotr

last: Topilko

first: Veronique

last: Tanty

first: Corinne

last: Blugeon

manufacture_protocol:
Slide spotted using a MicroGrid II (Genomic Solution)
Spotting conditions: Temperature of 20¡C more or less 5¡C. Hygroscopy of 50% more or less 5%.
Before each spotting:
1.	Printing tips (Geneworx 10k) are tested on glass slides.
2.	The spotting robot is put in operation and water tanks filled with distilled water.
3.	Corning glass slides are deposited on plates.
4.	The spotting program specific for each slide bacth is launched.


title: Salmonella typhimurium 4.5K

city: Bangalore

first: Dipshikha

last: Chakravortty

state: Karnataka

address: C.V.Raman AVENUE

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Amit

last: Lahiri

first: Priyanka

last: Das

manufacture_protocol: Refer manufacturer's web site http://www.chem.agilent.com


title: University of Tasmania Listeria monocytogenes 3K

status: Public on Jun 07 2007

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

institute: University of Tasmania

organism: Listeria monocytogenes

description: Custom oligo set based on Listeria monocytogenes EGD-e (cat. no. 812002) and control probe set (cat. no. 812099). Oligos were arrayed with quill pens at the Australian Genome Research Facility, Inc., Walter & Eliza Hall Medical Institute, Level 7, 1G Royal Parade, Parkville, Melbourne, Victoria, 3050, Australia

middle: P

first: Claudio

last: Bittencourt

first: Tom

last: Ross

manufacture_protocol:
70 bp DNA oligonucleotides-based spotted array on glass slides. For full details of methodology contact Dr. Stephen Wilcox;
stephen.wilcox@agrf.org.au; Australian Genome Research Facility, Inc., Walter & Eliza Hall Medical Institute, Level 7, 1G Royal Parade, Parkville, Melbourne, Victoria, 3050, Australia.
RNA conversion to cDNA and postlabelling with Cy3 and Cy5 was performed with the SuperScript Indirect cDNA Labeling System (Invitrogen).
Prehybridization was performed in hybrization solution (25% vol./vol. formamide, 5 X SSC buffer – 0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0, 0.1% sodium dodecyl sulfate) containing 10 mg ml-1 bovine serum albumin for 45 min at 42°C. Slides were then rinsed twice in distilled water and air-dryed. Hybridisation was performed in a humid hybridisation chamber at 42°C for 16-20 h using a hybridisation solution containing 0.42 ug ul-1 human Cot1 DNA, 0.62 ug ul-1 polyA and 0.83 ug ul-1 salmon sperm DNA. Slides were washed at room temperature in 1 X SSC buffer containing 0.2% SDS for 5 min and again in 0.1 X SSC buffer containing 0.2% SDS for 5 min. The slides were then further washed twice in 0.1 X SSC buffer at room temperature for 2 min.  Slides were then dried and subsequently scanned using a GenePix 4000A scanner (Axon Instruments).


title: CNIO Human Oncochip 1.0 , 1.2 and 2.0

first: Mohit

last: Aggarwal

address: Melchor F. Almagro 3

institute: CNIO

manufacturer: Genomic Unit, Biotechnology Program, Spanish National Cancer Research Centre

first: Miguel

last: Piris

manufacture_protocol:
1.- Individual I.M.A.G.E. Consortium [LLNL] clones were grown in 96-well plates at 37°C for 6 hours.
2.- The bacterial cultures were used for PCR amplification.
3.- PCR products were purified by ultrafiltration, verified by agarose gel electrophoresis and quantified by gel image densitometry
4.- Probe concentrations were adjusted in 50% DMSO at about 100-150 ng/ul.
5.- Probes were printed onto Gamma Amino Silane Coated glass slides (CMT-GAPS Corning) using the spotter Multigrid II (BioRobotics).
6.- After printing, the slides were baked for 4 hours at 80ºC and stored desiccated in the dark, under vacuum and at room temperature.


title: Whitehead-Young-Mouse-Solexa (ChIP-seq)

status: Public on Jul 30 2008

city: Cambridge

first: Whitehead

last: Institute

description:
Solexa sequencing
Data generated at Center for Advanced Genome Technology at Whitehead Institute using Genome Analyzer manufactured by Solexa/Illumina (Sequencing by Synthesis)

manufacture_protocol: not applicable