title: Broad-Mouse-Illumina-Genome-Analyzer-RRBS

status: Public on May 28 2008

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

organism: Mus musculus

technology: other

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

distribution: virtual


title: Drosophila melanogaster 19K 2002Jul23DrosoprintwithPatchedRelease020821

status: Public on May 29 2008

city: New Haven

first: Zareen

last: Gauhar

state: CT

address: 333 Cedar St, 386 NSB

department: Genetics

institute: Yale

organism: Drosophila melanogaster

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol: proprietary


title: Institute for Advanced Study Schizosaccharomyces pombe_44K_Nucleosome_Tiling_Array version1

status: Public on May 30 2008

city: San Francisco

first: Jun

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

organism: Schizosaccharomyces pombe

technology: in situ oligonucleotide

description: Nucleosome mapping in S. Pombe centromeres and histone-related genes.  Chromosome coordinates are with respect to the indicated small contigs and are based on the 2006 version of Sanger S. Pombe Genome Project

distribution: custom-commercial

first: Xingkun

last: Liu

first: Xiangwei

last: He


title: Broad-Mouse-Illumina-Genome-Analyzer-ChIPSeq

status: Public on May 27 2008


title: Institute for Advanced Study Schizosaccharomyces pombe_44K_Nucleosome_Tiling_Array2 version1


title: UCSF Mycobacterium tuberculosis oligo 3.9K

first: Michael

last: Shiloh

institute: University of California at San Francisco

organism: Mycobacterium tuberculosis

technology: spotted oligonucleotide

manufacturer: UCSF Center for Advanced Technology (CAT)

manufacture_protocol:
1.  Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in water to 20 uM and rearray 5 ÂµL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood).
4. Before printing, add 5 ÂµL of 1X Printing Buffer to each well. This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Incubate at 37Â°C for 30 minutes to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Centrifuge plates at 2000 rpm for 3 minutes.
9. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30 minutes before next cassette is needed to begin centrifugation.
10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
12. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 ÂµL per print run, as this is the amount drawn up by the pin capillary during each dip.


title: Listeria monocytogenes 13K I

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

organism: Listeria monocytogenes

manufacturer: Institute for Hygiene and Microbiology, University of Wuerzburg

first: Biju

last: Joseph

first: Sonja

last: Mertins

first: Regina

last: Stoll

first: Jennifer

last: Schär

first: Kanasinakatte

middle: R

last: Umesha

first: Qin

last: Luo

first: Stefanie

last: Müller Altrock

first: Werner

last: Goebel

manufacture_protocol:
oligonucleotides purchased from Operon Biotechnologies, Inc.

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 micromolar
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.
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
HANDLING OF PRINTED ARRAYS
The volume of washing solution should be at least 250 ml per 5 slides. Make sure that slides
do not dry out between washing steps, or between the washing and blocking step.
WASHING
1. Wash slides to remove unbound probe molecules and buffer substances to avoid
interference with subsequent hybridization experiments.
a. Rinse 1 x 5 min in 0.1% Triton X-100 at room temperature.
b. Rinse 2 x 2 min in 1 mM HCl solution at room temperature.
c. Rinse 1 x 10 min in 100 mM KCl solution at room temperature.
d. <optional> Denaturation step for arrays spotted with PCR-probes: 1 x 3 min in
boiling diH2O.
e. Rinse 1 x 1 min in diH2O at room temperature.
2. Proceed to Blocking immediately.
BLOCKING
1. Block the slides with Nexterion® Blocking Solution or alternatively with 50 mM
ethanolamine, 0.1% SDS (add freshly before use) in 0.1 M Tris, pH 9.0 as follows:
a. Incubate slides 1 x 15 min in 1x Nexterion® Blocking Solution at 50°C. The
volume of blocking solution should be at least 100 ml for 5 slides.
b. Rinse 1 x 1 min in diH2O at room temperature.
• Dry the Nexterion® Slide E in an oil-free air or nitrogen stream or by centrifugation
(200 x g for 5 min) to avoid any water stains on the slide surface.
• Proceed to hybridization.
HYBRIDIZATION
1. Re-suspend the dried, labeled target to be applied to the array in Nexterion® Hyb. In
case the target is already dissolved in a different buffer or in water, the sample can
also be diluted in Nexterion Hyb to get at least 90% (v/v) buffer in the final
hybridization solution.
2. Denature the suspended target by heating at 95°C for 3 min in a heat block, perform
a quick spin in a microcentrifuge, then pipette the appropriate volume onto the array
surface of a blocked slide under the coverslip or inside a hybridization station.
POST-HYBRIDIZATION WASHING
1. Place the array into a slide rack and immerse in a dish containing 2x SSC and 0.2%
SDS. Wash in the above solution 1 x 10 min at room temperature.
2. Wash 1 x 10 min in 2x SSC.
3. Wash 1 x 10 min in 0.2x SSC at room temperature.
4. Dry the array in an oil free air or nitrogen stream or by centrifugation (200 x g for 5
min) to avoid water stains on the slide surface.
5. Protect the array from light, dust and abrasion of the array surface, until ready for
scanning. Ensure that the laser and filter set of the scanner is compatible with the
fluorescent labeling of the probe molecules.


title: Solexa sequencing of small RNAs from short-beaked echidna (18-24 nt)

status: Public on May 21 2008

city: Cold spring Harbor

first: ravi

last: Sachidanandam

state: NY

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

organism: Tachyglossus aculeatus


title: Listeria monocytogenes 14.5K II


title: Drosophila melanogaster 19K 2001Nov18DrosoprintRelease020821


title: UCM-Medina-Montastraea faveolata-1310-v1

status: Public on May 31 2008

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

organism: Orbicella faveolata

manufacturer: University of California, San Francisco, Center for Advanced Technology

first: Jodi

middle: A

last: Schwarz

first: Monica

last: Medina

first: Christian

last: Voolstra


title: Invitrogen ProtoArray v3 protein microarray lot HA10732

city: Cleveland

first: Ovidiu

last: Marina

state: OH

address: 10900 Euclid Ave

department: School of Medicine

institute: Case Western Reserve University

organism: Homo sapiens

technology: spotted peptide or protein

description: For further information use the microarray ID (barcode) RS00038272 at http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Biomarker-Discovery/ProtoArray/ProtoArray-Lot-Specific-Information.html (or current lot-specific information link on website)

manufacture_protocol: Human Protein Microarray v3.0, contains about 5000 human proteins, with slight variations between lots of microarrays. Microarrays are printed in lots of about 100 microarrays. Proteins are printed in duplicate adjacent spots on a nitrocellulose coated slide. Proteins are expressed by baculovirus in an insect cell line. For more information please see the web link.


title: Invitrogen ProtoArray v3 protein microarray lot HA10753

description: For further information use the microarray ID (barcode) RS00172890 at http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Biomarker-Discovery/ProtoArray/ProtoArray-Lot-Specific-Information.html (or current lot-specific information link on website)


title: UCSF Whole Mouse Genome 41K

first: Yan

last: Zhang

address: 513 Parnassus Ave, HSE1001B

department: Microbiology and Immunology

institute: University of California, San Francisco

description:
Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene.

Arrays of this design have barcodes that begin with 16012694 or 2512694.

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).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene.

Arrays of this design have barcodes that begin with 16012694 or 2512694.

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).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: IntelliGene Cancer DNA chip

city: Gyeongju-si

first: Kyung-Oh

last: Doh

state: Gyeongsangbuk-do

address: 707 Seokjang-dong

department: Physiology

country: South Korea

institute: Dongguk University

manufacture_protocol: see manufacturer's web site


title: Childrens Hospital Boston/HussonLab_Mycobacterium_Tubcerculosis_htpX_StandardGrowth

status: Public on May 23 2008

city: Boston

first: Kevin

last: Conlon

address: 300 Longwood avenue

department: Infectious Disease

institute: Childrens Hospital Boston

manufacturer: TIGR. The Institute for Genomic Research

middle: M

first: Sahadevan

last: Raman

first: Robert

middle: N

last: Husson

manufacture_protocol: As supplied by TIGR with no modifications


title: AFFYMETRIX Human Chromosomes 21 & 22 v2.0b

status: Public on May 25 2008

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

manufacture_protocol: Affymetrix standard array manufacture protocol. Please refer to http://www.affymetrix.com/technology/manufacturing/index.affx for details.


title: Solexa sequencing of small RNAs from platypus (18-24 nt)

organism: Ornithorhynchus anatinus


title: Whole genome Leishmania spp. 9k microarray v1.0

city: Québec

first: Marc

last: Ouellette

state: Québec

address: 2705 bd Laurier

department: Département médecine

country: Canada

institute: Université Laval

organism:
Leishmania major
Leishmania infantum

description:
Centre de Recherche en Infectiologie du CHUL. Leishmania 9K v1.0.
The array was designed to detect with 2 mismatches or less all genes from Leishmania infantum and Leishmania major.

manufacturer: BIOGEM (BioMedical Genomics Microarray Facility), University of california

first: Frederic

last: Raymond

manufacture_protocol:
70-mer oligonucleotides probes were designed for each open reading frame of L. infantum and/or L. major
The microarrays were printed on SuperChip (Erie Scientific) using a BioRobotics Microgrid (Genomic solutions Inc). Pin type: Micro-Spot 10K split pins. We used 48 matched pins.
Each probe was printed in duplicate. The fill volume was 55 nl of oligos at 50uM in 50%DMSO.


title: Solexa sequencing of small RNAs from platypus (25-33 nt)


title: LC-sense 284 chip


title: LC-sense 5K chip


title: Pectobacterium atrosepticum 4.5K Eca4444Array

status: Public on May 24 2008

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism: Pectobacterium atrosepticum

manufacture_protocol: Agilent inkjet technology, 60mer oligos


title: NIMH, CBDB Illumina Sentrix Array Matrix _1.4k

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

technology: oligonucleotide beads

description:
A custom microarray (Illumina Sentrix Array Matrix or SAM) was designed and constructed to interrogate the expression of the selected genes in addition to many other genes relevant to neural function. The total number of unique probes included in the microarray was 1,379. The arrays consist of randomly assembled arrays of 3-micron bead features, each coated with a 50-nucleotide DNA probe. All the features are quality controlled by a sequential hybridization process called array decoding. Two unique probes were designed for each target sequence, and each probe was included on the array an average of 30 times.

The full array layout file is appended below as a supplementary file.


title: AFFYMETRIX Human ENCODE Chromosomes 1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,18,19,20,21,X v2.0


title: UHN Saccharomyces cerevisiae 6.4K v6 (Y6.4Kv6)

city: Emeryville

first: Mario

last: Ouellet

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

organism: Saccharomyces cerevisiae

manufacturer: University Health Network Microarray Center

manufacture_protocol: Double-spotted array containing 6,240 yeast ORFs (plus control spots totalling 6.4K). Detailed information about the ORFs and sequences can be found at the Saccharomyces Genome Database.  Clone set from Research Genetics Genepairs was PCR amplified and DNA purified. Printed on UltraGAPS ™ slides (Corning).


title: Boothroyd Lab Toxoplasma gondii bradyzoite 4K

status: Public on May 22 2008

city: Stanford

first: Jon

last: Boyle

address: 299 Campus Drive

institute: Stanford University School of Medicine

organism: Toxoplasma gondii

middle: P

first: Michael

last: Cleary

first: Upinder

last: Singh

first: Ira

last: Blader

first: John

middle: C

last: Boothroyd

manufacture_protocol: PCR products (generated by using 5 µl of overnight bacterial culture as a template) were ethanol precipitated, dried, resuspended in 3x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), and spotted onto poly-L-lysine-treated glass slides.


title: Invitrogen ProtoArray v3 protein microarray lot HA10726

first: Ovidiu

last: Marina

description: For further information use the microarray ID (barcode) RS00030883 at http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Biomarker-Discovery/ProtoArray/ProtoArray-Lot-Specific-Information.html (or current lot-specific information link on website)

manufacture_protocol: Human Protein Microarray v3.0, contains about 5000 human open reading frames, with slight variations between lots of microarrays. There are also control spots including GST and buffer. Microarrays are printed in lots of about 100 microarrays. Proteins are printed in duplicate adjacent spots on a nitrocellulose coated slide. Proteins are expressed by baculovirus in an insect cell line. For more information please see the web link.


title: UCFS Mycobacterium tuberculosis oligo 4.3K

last: Shiloh


title: CGH-SANGER Homo sapiens 4K 3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
The array contains 4099 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 4041 BACS are from the Sanger institute (Origin = CHORI or SANGER). 58 BACS were provided by K.U.Leuven Department CME (Origin = VIB4).
The bacs were amplified by DOP - PCR. In total the array design contains 8832 features printed in a layout of 4 meta rows, 4 meta columns, 23 rows per block and 24 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

first: Guy

last: Froyen

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1.	Microgrid (Genomics Solutions, UK).
2.	384 microtiter plates (X7022, Genetix)
3.	48 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4.	Codelink slides (cat# 30001100, GE Healthcare).
Printing 2 array of 4x4 blocks on 1 microscope slide:
1.	Dissolve PCR products in 250mM Phosphate buffer, 0.00025% sarcosyl at concentrations ranging between 300 and 600 ng/ul and array in 384 microtiter plates.
2.	Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55-60%; 123 spots per source visit.
3.	Make sure room temperature is between 20-24 degrees Celsius.
4.	Place microtiter plates in the plate hotel with A1 in front left corner.
5.	Place 60 slides on the slide-deck.
6.	Start spotting early in the morning and continue over night. Leave spotter overnight with vaccuum and humidity settings on. Empty the spotter the next morning.
7.	After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH, 0.1% SDS, H2O.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: SalkGAL-Arabidopsis-IlluminaGA-epigenome - small RNA sequencing and 5'-RACE sequencing

status: Public on May 15 2008

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

organism: Arabidopsis thaliana

description: Genetic Analyzer, Illumina, San Diego, CA


title: CGH-SANGER Homo sapiens 4K 4

description:
The array contains 4066 distinct BAC and PAC sequences. 4008 BACS are from the Sanger institute (Origin = CHORI or SANGER). 58 BACS were provided by K.U.Leuven Department CME (Origin = VIB4). The bacs from SANGER and VIB4 were printed in 2 replicates; the clones from CHORI with 4 replicates.
The bacs were amplified by DOP - PCR. In total the array design contains 10080 features printed in a layout of 12 meta rows, 4 meta columns, 15 rows per block and 14 columns per block.

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1.	Microgrid (Genomics Solutions, UK).
2.	384 microtiter plates (X7022, Genetix)
3.	48 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4.	Codelink slides (cat# 30001100, GE Healthcare).
Printing 1 array of 12x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 250mM Phosphate buffer, 0.00025% sarcosyl at concentrations ranging between 300 and 600 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 1 array of 12x4 blocks printed with 16 pins: column pitch = 230 um, row pitch = 230 um; Humidity 55-60%; 123 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 slides on the slide-deck.
6. Start spotting early in the morning and empty the spotter at the end of the day.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH, 0.1% SDS, H2O.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 15

status: Public on May 14 2008

first: Thomas

last: Gingeras


title: Drosophila melanogaster 19K 2002Sept24DrosoprintwithPatchedRelease021101

first: Zareen

last: Gauhar

institute: Yale


title: Print_1093

status: Public on May 20 2008

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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: Univ_of_Bologna_Mouse_120

status: Public on May 19 2008

city: Bologna

first: Elisabetta

last: Ciani

address: P.zza Porta San Donato, 2

department: Human and General Physiology

country: Italy

institute: University of Bologna

distribution: commercial

manufacture_protocol: 60-mer oligonucleotide probes printed on nylon membrane


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 16


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 14


title: Pelobacter carbinolicus antisense-detecting 12K oligo array

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

organism: Syntrophotalea carbinolica

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip.

first: Bradley

middle: L

last: Postier

first: Raymond

middle: J

last: DiDonato Jr.

first: Shelley

last: Haveman

first: Muktak

last: Aklukjar

manufacture_protocol: In-situ electrochemically synthesized oligonucleotide array. For reference see: Mauer et al., Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays. PLoS ONE. 2006, Dec 20;1:e34.


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 13


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 12


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 11


title: Print_933


title: Tavazoie Lab Escherichia coli 3.2k cDNA array

status: Public on May 13 2008

city: Princeton

first: yirchung

last: Liu

state: NJ

address: 220 Carl Icahn Laboratory

department: Molecular Biology

institute: Princeton University

organism: Escherichia coli K-12

description: The Platform data table reflects a condensed representation of the duplicate-spotted PCR products on the physical array.

first: Saeed

last: Tavazoie

first: yir-chung

manufacture_protocol: We produced in-house DNA microarrays that contain PCR-amplified fragment of DNA derived from predicted open reading frames (ORFs) in the E. coli genome.  All PCR products were analyzed by electrophoresis on 1% agarose gels.  Reactions that resulted in undetectable PCR products were re-amplified using a lower annealing temperature. All PCR products from the final round of amplifications were precipitated with ethanol, then dissolved in 50% DMSO (100-150 μg/ml) and spotted onto Corning GAPS II slides using Affymetrix GMS 417 Arrayer (Santa Clara, CA) in duplicate on each slide. Arrayed slides were baked at 80˚ C for 2 hours and stored in a desiccator at room temperature under vacuum.


title: Porphyromonas gingivalis W83 array

city: Seoul

first: Ji-Hoi

last: Moon

address: 1 Hoeki-Dong, Dongdaemoon-Ku

department: Oral Microbiology

institute: School of Dentistry, Kyung Hee University

organism: Porphyromonas gingivalis

first: Jin-Yong

last: Lee

manufacture_protocol: The whole genome of 1,909 genes of P. gingivalis W83 (GenBank accession no. NC_002950) was submitted to NimbleGen System Inc. (Madison, WI, U.S.A.) for microarray design and manufacture using maskless, digital micromirror technology. Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each genes in the genome. 60-mer probes were selected such that each probe had at least three mismatches compared to all other 60-mers in the target genome. A quality control check (hybridization) was performed for each array, which contained on-chip control oligonucleotides. The arrays were analyzed using an Axon Gene Pix 4000B scanner with associated software (Molecular Devices Corp., Sunnyvale, CA). Gene expression levels were calculated with NimbeScan Version 2.3 (NimbleGen). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on quantile normalization method using the R package.


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 2

organism: Mus musculus


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 1


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 4


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 9


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 6


title: Print_996


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 5


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 10


title: YCU Human 4.2K version 1

status: Public on May 11 2008

city: Yokahama

first: Takeshi

last: Mizuguchi

address: Fukuura 3-9, Kanazawa-ku

department: Department of Human Genetics

country: Japan

institute: Yokohama City University

manufacturer: Department of Human Genetics, Yokohama City University

first: Noriko

last: Miyake

first: Naoki

last: Harada

first: Osamu

last: Shimokawa

first: Nadia

last: Sosonkina

first: Aiko

last: Okubo

first: Norio

last: Niikawa

first: Naomichi

last: Matsumoto

manufacture_protocol: We selected 4,219 'FISHed' BAC/PAC clones using UCSC genome browser [2004 May version (http://genome.ucsc.edu/cgi-bin/hgGateway)], spacing at every 0.75 Mb of the whole human genome. All clones spotted showed a unique signal at the predicted chromosomal location by FISH. BAC/PAC DNA was extracted using an automatic DNA extraction system PI-100 (Kurabo, Osaka, Japan), amplified by two-round DOP PCR. DOP-PCR was performed to amplify target-clone DNA using three different 1st DOP PCR primers, DOP-A: CCGACTCGAGNNNNNNATGTGG; DOP-B: CCGACTCGAGNN NNNNTTCAC C; DOP-C: CCGACTCGAGNNNNNNAACAGG. The second PCR was performed using the 5'-amino-labeled primer (GGAAACAGCCCGACTCGAG). Successfully amplified PCR products purified and adjusted to the final concentration >1 ug/μl, and spotted in duplicate on CodeLinkTM activated slides (Amersham Biosciences Corp, NJ) by the ink-jet spotting method (Nihon Gaishi, Nagoya, Japan). Each DNA was spot in duplicate on one slide.


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 3

first: Thomas

last: Gingeras


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 8


title: Print_1000

last: Stanford Microarray Database


title: Axtell_Arabidopsis_Degradome_v1 (454 sequenced)

status: Public on May 08 2008

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: Unique tags of 20 or 21nt length obtained from Col-0 wild-type A. thaliana.

first: Charles

last: Addo-Quaye

first: Tifani

middle: W

last: Eshoo

first: David

last: Bartel


title: Mermaid_Human_32K_CGH_v1.0

city: London

first: Christopher

last: Jones

address: Paul O'Gorman Building, 72 Huntley Street

department: Gynaecological Oncology

country: United Kingdom

institute: UCL EGA Institute for Women's Health

first: Ken

last: Choi

first: Tanya

last: Lebi

first: Simon

last: Gayther

manufacture_protocol:
BAC miniprep DNA from the entire 32K BAC clone set was sourced from CHORI. 1µl of CHORI-prepared BAC DNA was amplified with Genomiphi (GE Healthcare) in a 10µl reaction. Amplified DNA was purified using the Millipore PCR384 cleanup plates and resuspended in 30µl Genetix print buffer. All reactions were set up using Biomek2000 liquid-handling robotics in barcoded microtitre plates and tracked through the manufacturing process using a bespoke LIMS database.
Arrays were printed onto Corning Ultragaps slides with a modified Genetix QArray2 printing robot, equipped with a Parallel Synthesis print head and 48x  50µm Parallel Synthesis silicon pins. Humidity of 65% was maintained throughout printing, and other printing conditions were optimized to provide average feature diameters of approximately 100µm ±10µm. Printing was performed in a climate controlled, positive pressure, HEPA/activated charcoal filtered laboratory.


title: Axtell_Arabidopsis_Degradome_v1 (Solexa/Illumina sequenced)


title: Cambridge University Toxoplasma gondii 12k cDNA array

first: Jon

last: Boyle

description: GAPS II (Corning)

manufacturer: Department of Pathology, Cambridge University

first: Jeroen

last: Saeij

first: Jim

last: Ajioka

first: John

last: Boothroyd

manufacture_protocol: Approximately 12,000 cDNA clones were PCR amplified, resuspended in 3X SSC, 1.5M betaine and printed onto GAPS II slides (Corning, Netherlands), using a Lucidea Pro array printer (GE Healthcare Bio-Sciences, Amersham, UK) with a 48-pin tool. The slides were baked for 18 hours at 80°C and stored dessicated at room temperature. For 7,488 of the cDNAs, end-sequence data was obtained previously and is available in Genbank


title: Salmonella enterica 17K STv7bSws_MMCC

status: Public on May 16 2008

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

description: whole slide version of GPL4805

first: Steffen

last: Porwollik

first: Carlos

last: Santiviago

first: Pui

last: Cheng

first: Xiao-Qin

last: Xia

manufacture_protocol: Custom made Salmonella array


title: CNIO Mouse chip 27.6K 3.0

city: Madrid

first: Rocio

middle: G.

last: Urdinguio

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Pathology Program

country: Spain

institute: Spanish National Cancer Centre (CNIO)

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

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: CSIRO-Chicken-Solexa sequencing-embryo miRNA

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

organism: Gallus gallus

manufacture_protocol: high-throughput sequencing


title: FHCRC miRNA Array v1.8.1

city: Seattle

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

organism:
Physcomitrium patens
Populus trichocarpa
Arabidopsis thaliana
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Zea mays
Caenorhabditis briggsae
Caenorhabditis elegans
Bombyx mori
Anopheles gambiae
Drosophila melanogaster
Drosophila pseudoobscura
Apis mellifera
Danio rerio
Xenopus laevis
Xenopus tropicalis
Gallus gallus
Lemur catta
Ateles geoffroyi
Lagothrix lagotricha
Macaca mulatta
Macaca nemestrina
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Canis lupus familiaris
Sus scrofa
Bos taurus
Ovis aries
Mus musculus
Rattus norvegicus
Human betaherpesvirus 5
human gammaherpesvirus 4
Gallid alphaherpesvirus 2
Monodelphis domestica
Takifugu rubripes
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Saguinus labiatus
Schmidtea mediterranea
Tetraodon nigroviridis
Betapolyomavirus macacae

description: The array contains microRNA probes for multiple organisms annotated in the miRBase database (Release 8.1).

manufacture_protocol: The multi-organism array was manufactured by spotting the contents of v8.1 of the miRCURY LNA Array ready to spot probe set from Exiqon onto glass microscope slides.


title: Bemisia tabaci 5.7K

city: Bet Dagan

first: Murad

last: Ghanim

address: Hamacabim

department: Entomology

country: Israel

institute: Volcani Center

organism: Bemisia tabaci

manufacturer: Ghanim Laboratory, Volcani Center, Israel

first: Assaf

last: Mahadav

first: Dan

last: Gerling

first: Yuval

last: Gottlieb

first: Henryk

last: Czosnek

manufacture_protocol:
Detailed description about manufacturing the array was provided in this reference:
Ghanim, M. and Kontsedalov, S. 2007. Gene expression in pyriproxyfen-resistant Bemisia tabaci Q biotype. Pest Manag Sci. 63:776-83. PMID: 17569108


title: Whitehead Institute Human Operon/Qiagen v3.1 oligonucleotide array

status: Public on May 12 2008

city: Cambridge

first: Whitehead

last: Institute

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

manufacturer: Whitehead Institute's Center of Microarray Technology


title: Yale-Illumina-Yeast-RNA-Seq

status: Public on May 05 2008

city: New Haven

first: Zhong

last: Wang

address: 266 Whitney Avn, KBT716

department: MCDB

institute: Yale University

description: Illumina 1G high throughput sequencing


title: BRI-NRC C. albicans expression microarray

status: Public on May 10 2008

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

organism: Candida albicans

manufacturer: National Research Council Canada - Biotechnology Research Institute

manufacture_protocol:
Probe design was done using a sliding window of 70 bp moved from the 3' -> 5' end of the target sequence. Self-annealing was calculated at each position as well as the GC count. A pre-computed cumulative mask of all the significant alignments found in the genome was made to favour regions that are unique for each genomic region.
Oligos were resuspended at 22 µM concentration in 50% DMSO and spotted on Corning Ultragaps slides with a BioRad ChipWriter Pro microarray spotter equipped with 48 SMP3 pins (Telechem ArrayIt). UV crosslinking (600 mJ) was performed in a Stratagene UV Stratalinker.


title: C. neoformans serotype D Cnba microarray

status: Public on May 07 2008

city: Bethesda

first: Yun

last: Chang

address: 10 Center Dr.

institute: NIH

organism: Cryptococcus neoformans

manufacturer: Microarray Facility of the Washington University Genome Sequencing Center

manufacture_protocol: The microarrays contain long oligomers (70-mers) that are designed to uniquely represent each gene in C. neoformans serotype D (one oligo per gene). These oligomers are arrayed on treated glass slides using split pin technology, together with oligomers representing a selection of host organisms (human, mouse, rat, rabbit, D. melanogaster, C. elegans, Dictyostelium and A. castellanii) and control oligos that represent unique Arabidopsis thaliana genes (commercially available RNA samples (Stratagene)). See website: http://128.252.233.3/activity/ma/cneoformans/


title: NKI/VanSteensel_HSA_390k_8/8_v070724

status: Public on May 06 2008

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

organism: Homo sapiens

description: Non-repetitive part of Human chromosomes HSA3, HSA9, HSAY. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 8 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.

first: Ludo

last: Pagie

first: Lars

last: Guelen

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: Custom LC Sciences Arabidopsis microRNA and SiRNA array

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

first: Sihui

last: Zhong

first: Qun

last: Li

first: Zuhua

last: He

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on August 2, 2005).
See http://www.lcsciences.com for additionnal details.
Some SiRNA probes were from ASPR (http://asrp.cgrb.oregonstate.edu/), another were designed according to the sequence information of NRG1 gene (Zuhua He et al., Science, 2000, Vol.288, pp.2360-2363)
LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a Paraflo microfluidic chip.


title: Affymetrix non-commercial Mouse Tiling 1.0 Array 7

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

manufacture_protocol: Affymetrix standard array manufacture protocol. Please refer to http://www.affymetrix.com/technology/manufacturing/index.affx for details.


title: NKI/VanSteensel_HSA_390k_7/8_v070724

description: Non-repetitive part of Human chromosomes HSA10, HSA11, HSA15. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 7 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: NKI/VanSteensel_HSA_390k_chr4_v070809

description: Non-repetitive part of Human chromosomes HSA4. Probe spacing approximately 200bp. Based on Human genome sequence NCBI 36.


title: NKI/VanSteensel_HSA_390k_6/8_v070724

description: Non-repetitive part of Human chromosomes HSA8, HSA16, HSAX. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 6 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: NKI/VanSteensel_HSA_390k_1/8_v070724

description: Non-repetitive part of Human chromosomes HSA1, HSA13, HSA22. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 1 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: NKI/VanSteensel_HSA_390k_3/8_v070724

description: Non-repetitive part of Human chromosomes HSA6, HSA12, HSA20. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 3 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs_ENTREZG_10]

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
Oligonucleotide probes on GeneChips were reorganized based on the latest genome and transcriptome information. In this particular case the Entrez Gene database (build: Sept 11, 2006) was used as source.
For the CDF file based on Entrez Gene:
A probe must hit only one genomic location;
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon.
For detailed description please see the paper and website.

first: Guido

last: Hooiveld

first: Philip

last: de Groot

manufacture_protocol: This array is identical to GPL570 but a custom, remapped CDF environment is used to extract data. This is version 9 of the remapped CDF. The CDF for various platforms can be found at the link below.


title: CGH-SANGER 3K 9

status: Public on May 02 2008

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description:
The array contains 3656 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 3573 BACS are from the Sanger institute. 83 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR. In total the array design contains 7744 features printed in a layout of 4 meta rows, 4 meta columns, 22 rows per block and 22 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: NKI/VanSteensel_HSA_390k_2/8_v070724

description: Non-repetitive part of Human chromosomes HSA2, HSA14, HSA21. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 2 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: NKI/VanSteensel_HSA_390k_4/8_v070724

description: Non-repetitive part of Human chromosomes HSA4, HSA5. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 4 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.


title: Splitter_Bmelitensis_289mini_v1

status: Public on May 01 2008

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin - Madison

organism: Brucella melitensis

first: Gireesh

last: Rajashekara

first: Amy

last: Rambow-Larsen

manufacture_protocol: Oligonucleotides (70-mers) representing 289 genes (Qiagen) were re-suspended in 3x SSC and spotted onto Ultra GAPS coated slides (Corning) using the MicroGrid Microarrayer (Apogent Discoveries). Slides were dessicated in a vaccum oven with Drierite for 48 hours and UV cross linked using a Stratalinker at 600mJ.  The printing of each ORF spot was verified by hybridizing with Cy3 labeled 9 mer (Qiagen).


title: Rosetta/Merck Dog 50k v2.0 Array 1 microarray

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Canis lupus familiaris

description: Contains 60-mer probes (60-mer).

first: John

last: Castle


title: Clostridium acetobutylicum ATCC824 oligomer ChIP 44k v3

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

organism: Clostridium acetobutylicum

description: The design algorithm for 60-mer oligonucleotides was based on a previously published algorithm that tests oligomers from multiple design programs (Paredes, Senger et al., 2007).

first: Carlos

last: Paredes

first: Ryan

last: Senger

middle: T

manufacture_protocol: see the manufacturer's website


title: NKI/VanSteensel_HSA_390k_5/8_v070724

first: Bas

last: van Steensel

description: Non-repetitive part of Human chromosomes HSA7, HSA17, HSA18, HSA19. Probe spacing approximately 750bp. Based on Human genome sequence NCBI 36. Platform 5 of 8, covering the whole human genome. Includes 9731 probes common to all 8 arrays of this series, used for between array normalization.

first: Ludo

last: Pagie

first: Lars

last: Guelen


title: Mycobacterium tuberculosis AROS, Operon Biotechnologies, Inc.

status: Public on May 03 2008

city: Aurora

middle: William

last: Honaker

state: CO

department: Microbiology

institute: University of Colorado Denver

organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

manufacturer: TB Vaccine Testing and Research Material Contract HHSN266200400091c

first: Richard

last: Slayden

manufacture_protocol:
1.Oligos are arrayed in Whatman 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Oligos are suspended in 3xSSC to 20 uM and centrifuged at 500 rpm for 2 minutes.
3. Plates are stored at 4oC overnight.
4. Incubate at RT for 30 minutes to aid resuspension of DNA.
5. Centrifuge plates at 500 rpm for 2 minutes.
6. Remove seals and cover plates with lids.
7. Print
8. After completion of print, allow slides to dry through passive evaporation in a protected environment.


title: Agilent-016809 Custom Human 244K CGH Microarray

first: Nick

last: Sampas

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

description: Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides mapped to UCSC hg17 human genome (NCBI build 35).

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


title: Bruguiera gymnorhiza 12k oligo microarray

city: Hachioji

first: Yuichi

last: Tada

state: Tokyo

address: 1404-1 Katakura

institute: Tokyo University of Technology

organism: Bruguiera gymnorhiza

description: see http://www.combimatrix.com/products_customarray.htm

first: Takuya

last: Yamanaka

first: Masashi

last: Miyama

manufacture_protocol: CustomArray™ uses a specially modified “CMOS” semiconductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in-turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the microelectrodes, and thus, the detritylation pattern applied on the chip during synthesis.


title: Clostridium botulinum ATCC3502 oligomer transcriptional 22k v1

organism: Clostridium botulinum

first: Shawn

last: Jones

first: Marite

last: Bradshaw

first: Eric

last: Johnson


title: Clostridium botulinum ATCC3502 oligomer transcriptional 44k v1


title: Clostridium acetobutylicum ATCC824 oligomer transcriptional 44k v3


title: SKI Drosophila melanogaster small RNA sequenced by Solexa

city: New York

first: Wei-Jen

last: Chung

address: 430 E 67th St

department: Developmental Biology

institute: Sloan-Kettering Institute

organism: Drosophila melanogaster

last: Lai


title: Aspergillus fumigatus 10.5k array v1_designed primarily based on strain Af293

status: Public on Feb 05 2008

city: San Jose

first: Jata

last: Shankar

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

organism: Aspergillus fumigatus

manufacturer: TIGR PFGRC (The Institute for Genomic Resource Pathogen Functional Genomics Resource Center)

first: Taruna

last: Madan

manufacture_protocol: QAF, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: MMAJ

status: Public on Dec 01 2007

city: Stanford

first: Howard

last: Chang

address: CCSR 2142

department: Dermatology

manufacturer: Joan,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu

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


title: National Cancer Institute ROSP Human 8k array

status: Public on Apr 02 2008

city: Gaithersburg

first: Shuping

last: Zhao

address: 8717 Grovemont Circle

department: Radiation Oncology Branch

institute: NCI

manufacturer: National Cancer Institute, Radiation Oncology branch, Microarray lab

manufacture_protocol: The microarrays used for the experiments contained 7,680 human cDNA clones and were prepared from Research Genetics Named Genes set (Huntsville, AL). These cDNA clones are enriched for known genes. All 7,680 cDNAs were spotted onto poly-L-lysine-coated slides (National Cancer Institute ROSP 8,000 Human Array) according to Eisen & Brown (Eisen, M. B., and Brown, P. O. DNA arrays for analysis of gene expression. Methods Enzymol., 303: 179–205, 1999.) using an OmniGrid arrayer (GeneMachines, San Carlos, CA).


title: Cardiff Array Facility print of the NIA 15K set, print format 1

status: Public on Aug 02 2007

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

institute: Cardiff University

description: Slides contain 17136 spots, printed in 12x4 mini grids, each with 17 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 (EmptyB). Landmarks were used to align the grids, Scorecard UT3 spots are for use with a spike control. Spots actually marked as "empty" were printed with water/DMSO.

manufacturer: Cardiff University Array Facility, Cardiff University and Wales Gene Park

first: Anna

last: Hurley

first: Victoria

last: Workman

first: Steven

last: Turner

first: Martin

last: Evans

first: Peter

last: Kille

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: HGMP NIA 15K set, format 2

status: Public on Aug 15 2007

description: HGMP printed NIA 15K arrays, printed on 2 slides, 17280 spots per slide, including control spots, empties and landmarks. 2 duplicate spots per slide for each clone. Earlier versions of these slides have already been described by platform entries GPL5457 and GPL5458. However, owing to analysis of a later array print run by a different image analysis programme in this series of experiments, the data files present in a different clone order and it is impossible to sort them to generate the same order. Hence this new platform submission. For ease of analysis, this platform entry combines Slides one and Two, (which are always hybed in pairs with the same hybe solution anyway)

first: Susan

last: Hunter

first: Carl

last: Daly

manufacture_protocol:
cDNA arrays (now discontinued), spotted PCR product. Bacterial source material diluted 1/10 prior to PCR,
primers: Ko forward primer (amidated): GTG TGG AAT TGT GAG CGG ATA ACA A (25mer) with 5' NH2(C6) modification.
Ko reverse primer: CCA GTC ACG ACG TTG TAA AAC GAC (24mer). Purified using Millipore Multiscreen PCR plates. Purified PCR products have then been rearrayed into 384 well plates and printed. 20µl of spotting buffer is added to 10µl of PCR product (0.1ug/ul) and this is sufficient to grid over 1000 glass arrays.
The manufacturers ask that the following paper describing the clones is cited in connection with these arrays: Tanaka TS, et al Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. PNAS (2000) 97: 9127-32


title: cph

status: Public on Oct 20 2006

last: Brotcke

state: CA

department: Microbiology and Immunology

organism: Francisella tularensis

manufacturer: Janos,,Demeter; Dept. Genetics, CCSR 2255, Stanford, CA, USA, 94305; 726-0075; jdemeter@genome.stanford.edu


title: HGMP NIA 15 K, slide 21-40 (2 of 2). Printed by HGMP, Hinxton

status: Public on Jul 11 2007

organism: Mus musculus

description: Second slide of 2. HGMP printed NIA 15K set, over 2 slides, 17280 spots per slide, including empties, control spots, landmark spots, and duplicate experimental spots. 12 rows and 4 columns of grids, each grid contains 18 rows and 20 columns of spots (format for both slides 1-20 and 21-40).

manufacture_protocol:
cDNA arrays (now discontinued), spotted PCR product. Bacterial source material diluted 1/10 prior to PCR,
primers: Ko forward primer (amidated): GTG TGG AAT TGT GAG CGG ATA ACA A (25mer) with 5' NH2(C6) modification.
Ko reverse primer: CCA GTC ACG ACG TTG TAA AAC GAC (24mer). Purified using Millipore Multiscreen PCR plates. Purified PCR products have then been rearrayed into 384 well plates and printed. 20µl of spotting buffer  is added to 10µl of PCR product (0.1ug/ul) and this is sufficient to grid over 1000 glass arrays.
The manufacturers ask that the following paper describing the clones is cited in connection with these arrays: Tanaka TS, et al Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. PNAS (2000) 97: 9127-32


title: SAGE:10:NlaIII:Bombyx mori

status: Public on May 19 2005

last: GEO

organism: Bombyx mori

technology: SAGE NlaIII

description:
This is a virtual platform for SAGE libraries generated for Bombyx mori using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: NIA 15 K set arrays, printed by HGMP, Hinxton, UK. Slide 1-20 (1 of 2)

description: HGMP printed NIA 15K arrays, printed on 2 slides, 17280 spots per slide, including control spots, empties and landmarks. 2 duplicate spots per slide for each clone. This is the platform submission for Slide 1


title: CE_printV

status: Public on Sep 13 2006

city: Palo Alto

first: Michael

last: Shapira

address: 300 Pasteur Dr. Lane Bldg. room L309

department: Genetics

organism: Caenorhabditis elegans

manufacturer: John,,Matese; Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Room 135, Princeton, NJ, United States; (609) 258-8309; jcmatese@genomics.princeton.edu


title: SAGE:10:NlaIII:Drosophila pseudoobscura

status: Public on Jun 13 2005

organism: Drosophila pseudoobscura

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


title: SAGE:22:NlaIII:Musa acuminata

status: Public on Jun 14 2005

organism: Musa acuminata

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


title: SAGE:10:NlaIII:Drosophila melanogaster

status: Public on Feb 23 2005

description:
This is a virtual platform for SAGE libraries generated for Drosophila melanogaster using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: Sigma PanoramaTM Mouse Apoptosis Gene Arrays

status: Public on Aug 11 2007

description: The array consists of 243 different apoptosis related cDNAs printed as PCR products onto charged nylon membranes. Each gene is printed in duplicate at 10 ng per spot. The array contains coding sequence specific PCR products derived from fully sequence characterized cDNA clones. Amplified gene sequences are free of Alu style repeats. The array also includes 7 housekeeping gene positive controls, mouse genomic DNA at the corners for positioning, and 5 negative controls

first: Jenny

last: Geatrell

last: Wride

manufacture_protocol: This macro-array consists of 243 different apoptosis related cDNAs printed as PCR products onto charged nylon membranes. Each gene is printed in duplicate at 10 ng per spot. See also Description.


title: SAGE:17:NlaIII:Magnaporthe grisea 70-15

status: Public on Nov 01 2004

organism: Pyricularia oryzae 70-15

description:
This is a virtual platform for longSAGE 17 libraries generated for Magnaporthe grisea (stain 70-15) using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: Siomi Lab fruit fly S2 AGO2 Annotation Results v1.0 (454 sequencing).

status: Public on May 08 2008

city: Koto-ku

first: Toutai

last: MITUYAMA

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Drosophila endogenous small RNAs bind to Argonaute2 in somatic cells 2008 Annotation Results

first: Yoshinori

last: Kawamura

first: Kuniaki

last: Saito

first: Taishin

last: Kin

first: Yukiteru

last: Ono

first: Kiyoshi

last: Asai

first: Takafumi

last: Sunohara

first: Tomoko

last: Nagami-Okada

first: Mikiko

last: Siomi

first: Haruhiko


title: CE_printW


title: STM010710

status: Public on Nov 04 2005

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Salmonella enterica subsp. enterica serovar Typhimurium

manufacturer: Tina,,Boussard; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-736-0077; boussard@genome.stanford.edu


title: SAGE:10:NlaIII:Lentinula edodes

status: Public on Sep 20 2004

organism: Lentinula edodes

description:
This is a virtual platform for SAGE libraries generated for Lentinula edodes using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SAGE:17:NlaIII:Zea mays

status: Public on Sep 21 2004

organism: Zea mays

description:
This is a virtual platform for longSAGE 17 libraries generated for Zea mays using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: MMP

status: Public on Jul 09 2005

first: Oliver

last: Aalami

address: 257 Campus Dr.

manufacturer: Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu

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


title: MMAI

status: Public on Jun 07 2006

first: Justin

last: Odegaard

address: 269 Campus Dr

department: CCSR 3110

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: EHC

status: Public on Jul 22 2005

organism: Entamoeba histolytica

manufacturer: Catherine,,Ball; Stanford University School of Medicine, Department of Genetics, CCSR Room 2255b, Stanford, CA, USA, 94305; 650-498-6012; ball@genome.stanford.edu


title: SAGE:17:NlaIII:Caenorhabditis elegans

status: Public on May 28 2004

description:
This is a virtual platform for longSAGE 17 libraries generated for Caenorhabditis elegans using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SARST:Bacteria

status: Public on Jan 07 2004

organism: Bacteria

technology: SARST

description: This is a virtual platform for SARST libraries generated for Bacteria.


title: SAGE:10:NlaIII:Caenorhabditis elegans

description:
This is a virtual platform for SAGE libraries generated for Caenorhabditis elegans using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SAGE:14:RsaI:Mus musculus

technology: SAGE RsaI

description:
This is a virtual platform for SAGE libraries generated for Mus musculus using RsaI as an anchor enzyme.
Platform_anchor: RsaI


title: STMSTY1

status: Public on Mar 15 2006


title: NimbleGen Mouse 391K tiling array (NCBI36)

status: Public on May 10 2008

city: Seattle

first: Ze

last: Cheng

address: 1905 NE Pacific St.

department: Genome Sciences

institute: University of Washington

description:
We designed high density (1 probe/481 bp) CGH tiling array against mouse (mm8) segmental duplications and 10 kb of their flanking regions.
Platform annotation based on Mouse Genome Build 36.
The .ndf and .pos files are linked below as Supplementary files.

first: Xinwei

last: She

first: Anne

last: Morrison

first: Sebastian

last: Zöllner

first: Deanna

last: Church

first: Evan

middle: E

last: Eichler

manufacture_protocol: per Nimblegen protocol


title: SAGE:10:NlaIII:Zea mays

status: Public on May 20 2004

last: GEO

description:
This is a virtual platform for SAGE libraries generated for Zea mays using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII