title: AgResearch, Rumen Microbial Genomics_Bpr_Mru_20K_v1_Print 121

status: Public on Jan 28 2010

city: Urbana

first: Carl

middle: James

last: Yeoman

state: IL

address: 1207 W Gregory ave

department: Institute for Genomic Biology

country: USA

institute: University of Illinois

organism:
Butyrivibrio proteoclasticus B316
Methanobrevibacter ruminantium M1

technology: spotted oligonucleotide

distribution: non-commercial

middle: J

first: Zhanhao

last: Kong

first: William

last: Kelly

first: Graeme

middle: T

last: Attwood

manufacture_protocol:
70mer and 50mer oligonucleotide probes were designed to the ORFs identified by GLIMMER in the draft sequences of B. proteoclasticus and M. ruminantium using ROSO (Recherche et Optimisation de Sondes Oligonucleotidiques; Reymond et al. 2004; Available: [http://pbil.univ-lyon1.fr/roso]. Controls included Blanks, 8 Arabidopsis thaliana genes and randomly in-silico mutated genes from B. proteoclasticus. 70mer oligonucleotides meeting the design parameters of ROSO were
synthesized by Illumina (San Diego, CA, USA) and subsequently spotted in triplicate onto the surface of an epoxy coated slide (Corning, Lowell,
MA, USA) using an ESI robot (Engineer Service Inc., Toronto, Ontario, Canada). In addition to the 70mers, triplicate 50mers were also printed for genes deemed to be of most importance to this research program. Features were printed with 100 um diameter.  Hybridisation-ready microarrays were stored desiccated at room temperature until use.


title: Illumina Genome Analyzer (Acyrthosiphon pisum)

status: Public on Jan 29 2010

last: GEO

organism: Acyrthosiphon pisum

technology: high-throughput sequencing

distribution: virtual


title: Lewis-Sigler Institute Saccharomyces 13K [20080530MD_PMC]

status: Public on Jan 23 2010

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

description: SBSC print, a multi-organism print.

manufacturer: Lewis-Sigler Institute Microarray Facility

manufacture_protocol:
The following parameters were used to manufacture
the printed array named 20080530MD_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	16
Spot Rows per Sector:	17
Column Spacing:	235
Row Spacing:	242
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Print Replicate Spots:	1
Number of Slides:	254
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100700	SBSC_SONIC_1
100514	HYBRIDSC_2
100502	HYBRIDSB_3
100503	HYBRIDSB_4
100507	HYBRIDSB_8
100508	HYBRIDSB_9
100526	HYBRIDSC_14
100513	HYBRIDSC_1
100511	HYBRIDSB_12
100521	HYBRIDSC_9
100519	HYBRIDSC_7
100504	HYBRIDSB_5
100704	SBSC_SUPP_1
100522	HYBRIDSC_10
100518	HYBRIDSC_6
100520	HYBRIDSC_8
100500	HYBRIDSB_1
100501	HYBRIDSB_2
100523	HYBRIDSC_11
100515	HYBRIDSC_3
100506	HYBRIDSB_7
100529	HYBRIDSC_17
100505	HYBRIDSB_6
100525	HYBRIDSC_13
100512	HYBRIDSB_13
100528	HYBRIDSC_16
100524	HYBRIDSC_12
100509	HYBRIDSB_10
100510	HYBRIDSB_11
100517	HYBRIDSC_5
100527	HYBRIDSC_15
100516	HYBRIDSC_4
100700 	SBSC_SONIC_1


title: Illumina Genome Analyzer II (Miscanthus x giganteus)

status: Public on Jan 26 2010

organism: Miscanthus x giganteus


title: Lewis-Sigler Institute Saccharomyces 13K [20070608MD_PMC]

description: SBSC multi-organism print

manufacture_protocol:
The following parameters were used to manufacture
the printed array named 20070608MD_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	16
Spot Rows per Sector:	16
Column Spacing:	235
Row Spacing:	240
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Print Replicate Spots:	1
Number of Slides:	240
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100700	SBSC_SONIC_1
100506	HYBRIDSB_7
100512	HYBRIDSB_13
100526	HYBRIDSC_14
100501	HYBRIDSB_2
100515	HYBRIDSC_3
100519	HYBRIDSC_7
100529	HYBRIDSC_17
100509	HYBRIDSB_10
100507	HYBRIDSB_8
100500	HYBRIDSB_1
100524	HYBRIDSC_12
100513	HYBRIDSC_1
100504	HYBRIDSB_5
100514	HYBRIDSC_2
100517	HYBRIDSC_5
100521	HYBRIDSC_9
100510	HYBRIDSB_11
100505	HYBRIDSB_6
100523	HYBRIDSC_11
100508	HYBRIDSB_9
100520	HYBRIDSC_8
100503	HYBRIDSB_4
100516	HYBRIDSC_4
100525	HYBRIDSC_13
100511	HYBRIDSB_12
100522	HYBRIDSC_10
100528	HYBRIDSC_16
100502	HYBRIDSB_3
100527	HYBRIDSC_15
100518	HYBRIDSC_6
100700	SBSC_SONIC_1


title: Lewis-Sigler Institute Saccharomyces 12K [20061110_PMC]

description: SBSC multi-organism print

manufacture_protocol:
The following parameters were used to manufacture the printed array named 20061110_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	24
Spot Rows per Sector:	10
Column Spacing:	175
Row Spacing:	175
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Number of Slides:	252
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100505	HYBRIDSB_6
100512	HYBRIDSB_13
100509	HYBRIDSB_10
100508	HYBRIDSB_9
100501	HYBRIDSB_2
100502	HYBRIDSB_3
100503	HYBRIDSB_4
100511	HYBRIDSB_12
100510	HYBRIDSB_11
100506	HYBRIDSB_7
100504	HYBRIDSB_5
100500	HYBRIDSB_1
100507	HYBRIDSB_8
100525	HYBRIDSC_13
100514	HYBRIDSC_2
100518	HYBRIDSC_6
100517	HYBRIDSC_5
100521	HYBRIDSC_9
100522	HYBRIDSC_10
100527	HYBRIDSC_15
100528	HYBRIDSC_16
100516	HYBRIDSC_4
100515	HYBRIDSC_3
100513	HYBRIDSC_1
100523	HYBRIDSC_11
100526	HYBRIDSC_14
100524	HYBRIDSC_12
100529	HYBRIDSC_17
100519	HYBRIDSC_7
100520	HYBRIDSC_8


title: Illumina MouseWG-6 v2.0 expression beadchip [Alternative CDF: affy4248alt]

status: Public on Jan 11 2010

city: Philadelphia

first: Marni

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

organism: Mus musculus

technology: oligonucleotide beads

distribution: custom-commercial

relation: Alternative to: GPL6887 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6887 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.


title: SMD Print_1066 Homo sapiens

city: Amsterdam

first: Lisa

last: van Baarsen

address: Meibergdreef 9

department: Div. of Clinical Immunology and Rheumatology

country: Netherlands

institute: EULAR & FOCIS Center of Excellence

organism: Homo sapiens

technology: spotted DNA/cDNA

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: Lewis-Sigler Institute Saccharomyces 13K [20070627MD_PMC]

description: SBSC multi-organism print

manufacture_protocol:
The following parameters were used to manufacture the printed array named 20070627MD_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	16
Spot Rows per Sector:	16
Column Spacing:	235
Row Spacing:	240
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Number of Slides:	240
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100700	SBSC_SONIC_1
100508	HYBRIDSB_9
100516	HYBRIDSC_4
100503	HYBRIDSB_4
100520	HYBRIDSC_8
100518	HYBRIDSC_6
100505	HYBRIDSB_6
100523	HYBRIDSC_11
100510	HYBRIDSB_11
100521	HYBRIDSC_9
100517	HYBRIDSC_5
100514	HYBRIDSC_2
100504	HYBRIDSB_5
100513	HYBRIDSC_1
100527	HYBRIDSC_15
100502	HYBRIDSB_3
100528	HYBRIDSC_16
100522	HYBRIDSC_10
100511	HYBRIDSB_12
100525	HYBRIDSC_13
100500	HYBRIDSB_1
100524	HYBRIDSC_12
100509	HYBRIDSB_10
100507	HYBRIDSB_8
100519	HYBRIDSC_7
100529	HYBRIDSC_17
100501	HYBRIDSB_2
100515	HYBRIDSC_3
100526	HYBRIDSC_14
100512	HYBRIDSB_13
100506	HYBRIDSB_7
100700	SBSC_SONIC_1


title: SMD Print_1308 Homo sapiens

status: Public on Jan 21 2010

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich


title: SMD Print_1451 Homo sapiens


title: SMD Print_1060 Homo sapiens


title: MRC Human IIR 37 v1

city: Yokohama

first: Hiroyuki

last: Oshima

address: 10-1 Daikoku-cho, Tsurumi-ku

country: Japan

institute: Mitsubishi Rayon Co.,LTD

description: Oligo nucleotide probes were covalently attached to hydrophilic gel which bond to inner wall of plastic hollow fiber.

first: Tatsunobu

last: Fukushima

manufacture_protocol:
The oligonucleotide probes were designed by 37 of innate immune related genes and to be the same annealing temperature throughout a microarray. Probes were also designed within 1 kb from 3’-end of each genes.
To manufacture the DNA microarray of 37 genes, we used the Genopal(TM) (Mitsubishi Rayon) system as described below. Bundled plastic hollow fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel were embedded in resin, then polymerize and sliced it into thin chips.


title: MRC Human IIR 0.2K v1

manufacture_protocol:
The oligonucleotide probes were designed by 200 of innate immune related genes and to be the same annealing temperature throughout a microarray. Probes were also designed within 1 kb from 3’-end of each genes.
To manufacture the DNA microarray of 200 genes, we used the Genopal(TM) (Mitsubishi Rayon) system as described below. Bundled plastic hollow fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel were embedded in resin, then polymerize and sliced it into thin chips.


title: Custom Agilent Ciona intestinalis 2x22K Array

city: Kochi

first: Kaoru

last: Mita

address: 2-5-1, Akebono-cho

institute: Kochi University

organism: Ciona intestinalis

technology: in situ oligonucleotide

last: Azumi

manufacture_protocol: The microarray was manufactured by Agilent Technologies. The details can be found in their web site http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494


title: PGA/MGH mouse v1.1 oligonucleotide array

city: Dublin

first: Stephen

middle: Francis

last: Madden

address: Glasnevin

department: National Institute for Cellular Biotechnology

country: Ireland

institute: Dublin City University

manufacturer: Massachusetts General Hospital Microarray Core facility

manufacture_protocol: The PGA mouse v1.1 oligonucleotide probe sets (70-mers) were printed using an OmniGrid 100 printer (GeneMachines) on CodeLink-activated slides (Amersham). Oligos were printed in 150 mM sodium phosphate pH 8.5 with 0.0005% N-lauroyl sarcosine. Oligos were coupled to the activated slides by allowing the aminolinker on the oligos to react overnight in a humidity chamber. Unreacted groups on the slide surface were blocked with 150 mM glycine, 0.1 M tris, 0.1% N-lauroyl sarcosine, pH 9.


title: Lewis-Sigler Institute Saccharomyces 12K [20060831_PMC]

description: SBSC multi-organism print

manufacture_protocol:
The following parameters were used to manufacture the printed array named 20060831_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	24
Spot Rows per Sector:	10
Column Spacing:	176
Row Spacing:	174
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Number of Slides:	220
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100501	HYBRIDSB_2
100505	HYBRIDSB_6
100508	HYBRIDSB_9
100502	HYBRIDSB_3
100510	HYBRIDSB_11
100503	HYBRIDSB_4
100511	HYBRIDSB_12
100507	HYBRIDSB_8
100512	HYBRIDSB_13
100509	HYBRIDSB_10
100506	HYBRIDSB_7
100504	HYBRIDSB_5
100500	HYBRIDSB_1
100528	HYBRIDSC_16
100521	HYBRIDSC_9
100527	HYBRIDSC_15
100522	HYBRIDSC_10
100515	HYBRIDSC_3
100526	HYBRIDSC_14
100513	HYBRIDSC_1
100518	HYBRIDSC_6
100514	HYBRIDSC_2
100517	HYBRIDSC_5
100525	HYBRIDSC_13
100523	HYBRIDSC_11
100519	HYBRIDSC_7
100524	HYBRIDSC_12
100516	HYBRIDSC_4
100529	HYBRIDSC_17
100520	HYBRIDSC_8


title: [Mouse430_2] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Alternative CDF: affy9618alt]

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.


title: Aspen 7K Array version 2.1

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

organism: Populus

manufacture_protocol: 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.  Spots were printed with Corning Pronto! spotting solution at the Genomics Technology Support Facility of Michigan State University.   3. Spot layout: Each grid contains 12 spike controls on the top left corner. These include calibration controls (from high to low concentrations), ratio controls (different ratio combinations between Cy3 and Cy5 targets), and negative controls. Each grid contains 21×21 spots, except for the last row which has variable number of empty spots.  4. Spikes: To take advantage of the spike controls, appropriate spike mRNA samples need to be included during target labeling (see 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: ESTs were obatined from Populus tremuloides (Ranjan et al. 2004) or Populus fremontii x angustifolia. Sequence information can be obtained by searching the GenBank or our ESTdb (http://aspenDB.uga.edu) using the MTU clone IDs. As is the case for other large-scale projects, there are likely errors in the annotation.  6. This platform contains a non-redundant clone list from the full array (GPL6992).  Duplicate spots (EST clones in the subarrays or spike controls) are represented only once.                             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: UofT KB1 19.2K v2

status: Public on Jan 27 2010

city: Toronto

first: Elizabeth

middle: A

last: Edwards

address: 200 College st.

department: Department of Chemical Engineering and Applied Chemistry

country: Canada

institute: University of toronto

organism: dechlorinating enrichment culture KB-1

description:
KB1 mixed microbial consortium.  Composition of community as estimated by 16S qPCR:

Dehalococcoides:48.1-70.2%
Chlorobi SJA-28:6-14.9%
Acetobacterium:2.65-12%
Sporomusa:1.2-11.45%
Spirochaete SA-8 :2.8-8.3%
Methanomicrobiales:3.5-5.8%
OP5:2.5-5%
Geobacter:3-4.4%
Methanosarcina:0.1-1%
Methanosaeta:0-0%
Bacteroidales 1:0-0.8%
Syntrophus:0-0.03%
Syntrophobacter:0-0.2%
Sulfurospirillum:0-0.002%
Methanomethylvorans:0-0.04%

manufacturer: University Health Network (UHN) Microarray Facility, Toronto, Ontario, www.microarrays.ca

manufacture_protocol:
1 - gDNA was extracted from the mixed culture KB1, 1-3 kb fragments were eluted and purified from 1% agarose gel
2 - The fragments were then blunt-end repaired and dephosphorylated before undergoing blunt-end cloning.
3 - After transformation into E. coli, individual bacterial colonies were picked into  plates , and grown over night
4- PCR amplification of the inserts was performed using the E.Coli culture and T7f/M13r primers for the plasmid
5 - The PCR products were purified, quantified spectrophotometrically and then transferred to 384-well plate and adjusted to 200 ng/µl in 3XSSC buffer and sent for printing.
6- The amplicons were spotted with the VersArray ChipWriter Pro System (Bio-Rad, 169-0006) using a 48-pin (SMP-3 pins, ArrayIT, product #SMP3) configuration.
7 - Each clone was spotted once on GAPS II–coated slides (Corning, 40003).
8 - The printed arrays were processed following manufacturer’s protocol (Corning) and kept in a dessicator for later use.


title: Illumina mouse-6 v1.1 expression beadchip [Array_Address_Id version]

status: Public on Feb 14 2008

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

distribution: commercial

manufacture_protocol:
See manufacturers website
http://www.illumina.com


title: Illumina HumanOmni1 Genotyping BeadChip

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

manufacture_protocol: See manufacturer's website.


title: UMCU_IBUMAD_mssa476_5741feat_genecops

status: Public on Jan 24 2010

city: Bilthoven

first: Tessa

middle: E

last: Pronk

address: A.v Leeuwenhoeklaan 9

department: GBO

institute: RIVM

organism: Staphylococcus aureus subsp. aureus MSSA476

description: 8x15k slides

first: Wim

middle: C

last: de Leeuw

first: Floyd

last: Wittink

first: Timo

middle: M

last: Breit

manufacture_protocol:
Probes (60 nucleotides) were designed to target all coding genes of mssa476 as well as rRNA and intergenic regions not opposite of a gene using the webservice of Agilent (eArray). Probes were tested for cross-hybridization by a combined CGH and blast experiment.
Spotting was performed by Agilent. Spotting protocols were not provided.


title: NRC-BRI human 19K cDNA spotted array

status: Public on Jan 22 2010

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

description: 19,008 genes/ESTs

manufacturer: University Health Network (Toronto, ON, Canada)


title: Hubrecht Rat 2.1M HX1

status: Public on Jan 30 2010

city: Utrecht

first: Victor

last: Guryev

address: Uppsalalaan 8

institute: Hubrecht Institute

organism: Rattus norvegicus

description:
Genome assembly: RGSC3.4
native array description file: 080616_Cuppen_rat34_WG_CGH_HX1.ndf
native array description file: 080616_Cuppen_rat34_WG_CGH_HX1.pos

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: NHGRI Homo sapiens 28K cDNA array

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

manufacture_protocol: Arrays were constructed on glass slides from PCR products representing the inserts of 28,411 IMAGE consortium cDNA clones in the National Human Genome Research Institute microarray core laboratory.


title: 454 GS FLX (Tetraodon nigroviridis)

status: Public on Jan 19 2010

last: GEO

organism: Tetraodon nigroviridis


title: Lewis-Sigler Institute Saccharomyces 13K [20070907MD_PMC]

first: Maitreya

last: Dunham

description: SBSC multi-organism print

manufacture_protocol:
The following parameters were used to manufacture the printed array named 20070907MD_PMC
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	16
Spot Rows per Sector:	16
Column Spacing:	235
Row Spacing:	240
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Number of Slides:	250
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100700	SBSC_SONIC_1
100522	HYBRIDSC_10
100527	HYBRIDSC_15
100528	HYBRIDSC_16
100507	HYBRIDSB_8
100502	HYBRIDSB_3
100514	HYBRIDSC_2
100525	HYBRIDSC_13
100511	HYBRIDSB_12
100500	HYBRIDSB_1
100529	HYBRIDSC_17
100509	HYBRIDSB_10
100518	HYBRIDSC_6
100520	HYBRIDSC_8
100524	HYBRIDSC_12
100519	HYBRIDSC_7
100513	HYBRIDSC_1
100516	HYBRIDSC_4
100515	HYBRIDSC_3
100512	HYBRIDSB_13
100517	HYBRIDSC_5
100508	HYBRIDSB_9
100505	HYBRIDSB_6
100504	HYBRIDSB_5
100510	HYBRIDSB_11
100526	HYBRIDSC_14
100503	HYBRIDSB_4
100501	HYBRIDSB_2
100521	HYBRIDSC_9
100506	HYBRIDSB_7
100523	HYBRIDSC_11
100700	SBSC_SONIC_1


title: Illumina Genome Analyzer II (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: NRC-BRI C. albicans expression microarray V2.0

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: Illumina Genome Analyzer (Masticophis flagellum testaceus; Pantherophis obsoletus lindheimeri)

status: Public on Jan 15 2010

organism:
Pantherophis obsoletus lindheimeri
Masticophis flagellum testaceus


title: Illumina Genome Analyzer II (Tribolium castaneum)

status: Public on Jan 14 2010

organism: Tribolium castaneum


title: Illumina Genome Analyzer II (Uncinocarpus reesii)

organism: Uncinocarpus reesii


title: Illumina Genome Analyzer (Arabidopsis thaliana; Cucumber mosaic virus (strain FNY))

status: Public on Jan 20 2010

organism:
Arabidopsis thaliana
Cucumber mosaic virus (strain FNY)


title: Illumina Genome Analyzer II (Volvox carteri)

organism: Volvox carteri


title: Illumina Genome Analyzer (Python regius)

organism: Python regius


title: Illumina Genome Analyzer (Crotalus atrox)

organism: Crotalus atrox


title: NimbleGen Human 2.1M array [HG18_CGH_LISOv1_HX1]

first: Jie

last: Tang

address: 120 Green St

department: Institute of Bioinformatics

description: Annotation in this record based on NCBI human build 36.


title: Illumina Genome Analyzer II (Postia placenta)

organism: Rhodonia placenta


title: Illumina Genome Analyzer II (Selaginella moellendorffii)

organism: Selaginella moellendorffii


title: Illumina Genome Analyzer II (Ciona intestinalis)

organism: Ciona intestinalis


title: Illumina Genome Analyzer II (Physcomitrella patens)

organism: Physcomitrium patens


title: Illumina Genome Analyzer II (Apis mellifera)

organism: Apis mellifera


title: Illumina Genome Analyzer II (Laccaria bicolor)

organism: Laccaria bicolor


title: Illumina Genome Analyzer II (Phycomyces blakesleeanus)

organism: Phycomyces blakesleeanus


title: Illumina Genome Analyzer II (Coprinopsis cinerea)

organism: Coprinopsis cinerea


title: University of Groningen Bacillus cereus ATCC 14579 5k array (condensed)

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Bacillus cereus ATCC 14579

description: The Platform data table reflects a condensed representation of the array's replicate features.

last: de Jong

manufacture_protocol: ArrayIt superamine slides spotted with a Genpak-array21 spotter.


title: Illumina Genome Analyzer II (Nematostella vectensis)

organism: Nematostella vectensis


title: Agilent/SNU human 24M CGH array, 2 of 24 (Feature Number version)

status: Public on Jan 13 2010

city: Seoul

first: Dongwan

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Genomic Medicine Institute, Seoul National University College of Medicine

organism: Homo sapiens

description:
Custom-designed 24M-oligonucleotide whole-genome array (1.1M X 24 slides).

Probes correspond to human genome build UCSC hg18 (NCBI Build 36).

manufacture_protocol: See manufacturer's web site (www.Agilent.com).


title: Agilent/SNU human 24M CGH array, 1 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 14 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 11 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 10 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 13 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 7 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 9 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 6 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 3 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 8 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 19 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 5 of 24 (Feature Number version)


title: Illumina Genome Analyzer II (Tetraodon nigroviridis)

organism: Tetraodon nigroviridis


title: NimbleGen Danio rerio 385K Zv7 tiling array

city: Shanghai

first: Yong

last: Zhang

address: 1239 Siping Road

country: China

institute: Tongji University

organism: Danio rerio

description:
UCSC zebrafish genome sequence Zv7
385K 50mer probes were printed and were spaced by 30 bp resulting in 80 bp resolution. Tiled regions include specifically selected genes (i.e. maternally provided genes, genes that are transcribed at zygotic genome activation, important developmental genes and known late genes) as well as two large contiguous genomic regions on linkage groups 3 and 11.
The .ndf and .pos files are linked below as supplementary files.


title: Agilent/SNU human 24M CGH array, 4 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 18 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 22 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 17 of 24 (Feature Number version)


title: Nimblegen Arabidopsis thaliana Whole Genome Tiling Array (385K) 3 of 3

status: Public on Jan 12 2010

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

institute: KAIST

organism: Arabidopsis thaliana

manufacture_protocol: see NimbleGen website at http://www.nimblegen.com


title: Agilent/SNU human 24M CGH array, 15 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 24 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 23 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 16 of 24 (Feature Number version)


title: IQ-USP Xylella fastidiosa 9.2K v2.0.

status: Public on Jan 06 2010

city: São Paulo

first: Paulo

middle: A.

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

organism: Xylella fastidiosa

manufacture_protocol: A 9,216-element DNA microarray was printed containing unique internal fragments of 2,608 CDS spotted at least in duplicate, representing 91.6% of all of the 2,848 CDS annotated by Simpson et al. (2000). DNA fragments ranging from 200 to 1,000 bp were PCR amplified with CDS-specific primers (18- to 23-mers) designed with PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) and based on the annotated genome sequence of X. fastidiosa strain 9a5c. PCR products in 50% DMSO were spotted with a Generation III Spotter (GE Healthcare, Little Chalfont, England) and kept in low humidity (<15%) until use.


title: Agilent/SNU human 24M CGH array, 21 of 24 (Feature Number version)


title: Agilent/SNU human 24M CGH array, 20 of 24 (Feature Number version)


title: Agilent Homo sapiens 8x15 array 15K

status: Public on Jan 03 2010

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

manufacture_protocol: Microarray probes were designed using eArray software (Agilent). Unique DNA probes specific to 486 human genes from the high density (HD) ChIP Database (Agilent) were included in each microarray. Microarray, 8x15K format, slides were custom manufactured by Agilent. Additional hybridization control probes (universal control grid LA577) were included in the arrays (Agilent). Each individual probe in the microarray was replicated 3-10 times.


title: The Genome Center at Washington University, Candida albicans 20K array

status: Public on Jan 04 2010

city: Worcester

first: Jessica

last: Lopes da Rosa-Spiegler

state: MA

address: 364 Plantation street

institute: University of Massachusetts Medical School

organism: Candida albicans

manufacturer: The Genome Center at Washington University (http://genome.wustl.edu/services/microarray/candida_albicans).

manufacture_protocol: See manufacturer's website


title: WCFS Lactobacillus plantarum 11K 60-mer array, Version 2

status: Public on Jan 01 2010

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

organism: Lactiplantibacillus plantarum WCFS1

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


title: Maize long oligonucleotide arrays 57K, version 1.13 Array B

city: Irapuato

first: June

last: Simpson-Williamson

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Plant Genetic Engineering

country: Mexico

institute: Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional

organism: Zea mays

description: similar to Platform GPL5440

manufacture_protocol:
REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS
1.Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 ?M oligonucleotide solution.
2.Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.
3.The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins.
4.Printing conditions:
Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides. The print head Z- velocity is set to a maximum of 10 mm/sec.
5.Bake slides for 2h at 80oC. Store dry and in darkness at RT.
The microarrays are sent out to recipient scientists at this point. Prior to hybridization, these next steps should be followed:
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS
1.Rehydrate the microarray slide over 50oC water for 5-10 seconds; snap-dry on a 65oC heating block for 5 seconds. Repeat this step 4-6 times, examining the slides under a dissection microscope (or using red reflectance imaging) to verify complete re-hydration of all the spots. If re-hydration is not complete, repeat the process several more times.
2.Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation. We employ a Stratalinker set at an energy level of 180 mJ.
Re-hydration and UV cross linking can be done well in advance before microarray hybridization, and the slides can be stored at room temperature for several months. However we do not recommend storage of washed microarray slides.
3.Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT.
4.Rinse the slides by plunging 10 times into sterile ddH2O.
5.Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking.
6.Spin dry the slides in a centrifuge at 1000 rpm for 2 min.
7.Store the slides in a light-proof box under cool dry conditions.


title: Strongylocentrotus purpuratus 8x15k (evidence-based array representing expressed genes from the blastula stage embryo)

status: Public on Jan 05 2010

city: Salisbury Cove

first: Anthony

last: Robertson

state: ME

address: Box 35 Old Bar Harbor Road

department: Functional Genomics

institute: Mount Desert Island Biolabs

organism: Strongylocentrotus purpuratus

description: The custom Array design was performed using Agilent eArray. Two 60-mer probes were designed to target each transcript from the blastula stage embryo.  Transcripts were derived from contiguous sequences that were assembled from ESTs derived from cDNA libraries.  The NCBI gene symbol and ID were subsequently mapped to each feature on the array as a deliberate means to facilitate retrieval of functional gene information at NCBI.

first: Alison

last: Coluccio

first: Benjamin

middle: L

last: King

first: James

last: Coffman

manufacture_protocol:
The microarray was manufactured by Agilent Technologies. The details can be found in their web site
http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_ENST, version 10]

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

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 Ensembl Transcript Ids (Ensembl build: 46) was used as source. For the CDF file: 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.

relation: Alternative to: GPL570 (Alternative CDF [official])


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [Alternative CDF: affy10736alt]

status: Public on Jan 11 2010

city: Philadelphia

first: Marni

last: Falk

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

organism: Mus musculus

relation: Alternative to: GPL6096 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6096 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.


title: Drosophila pseudoobscura 25.7K

city: college park

first: Carlos Alberto

last: Machado

department: department of biology

institute: University of Maryland

organism: Drosophila pseudoobscura

manufacture_protocol: see the manufacturer's website


title: Illumina Genome Analyzer (Spermophilus parryii)

status: Public on Jan 08 2010

last: GEO

organism: Urocitellus parryii


title: Agilent/SNU human 24M CGH array, 12 of 24 (Feature Number version)


title: University of Guelph, 1152 CfMNPV genes array version 1

city: Guelph

first: Dan-Hui

last: Yang

state: Ontario

address: 488 Gordon Street

department: Dept. of Molecular and Cellular Biology

institute: University of Guelph

organism: Choristoneura fumiferana multiple nucleopolyhedrovirus

description:
The array included 292 oligonucleotide probes representing 146 CfMNPV ORFs, one for the coding strand and the other for the non-coding strand (for detection of antisense transcription). Purified CfMNPV viral genomic DNA in 10-fold serial dilutions was used as a positive control. A mixture of 20 viral oligonucleotides was served as a second positive control. The array included 2 oligos (At1 and At2) of Arabidopsis chlorophyll synthase for normalization between arrays, and 2 oligos (HAT4, YaaJ) as negative controls. The array also included 5 host insect internal control oligos. Each probe was printed in triplicate.

This array represents a condensed array. The full array layout linked as a supplementary file.

manufacturer: Biotechnology Research Institute, Montreal, Canada

first: Jondavid

middle: G

last: de Jong

first: Eva

last: Nagy

first: Basil

last: Arif

first: Peter

last: Krell

manufacture_protocol: Spotted 50-mer nucleotides on glass slides


title: miRNA 3.7K microarray V3.0

city: peking

first: bing

last: shi

address: NO 39 huayuan north road

department: department of cardiology

institute: peking university third hospital

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: GEMO S. Pombe expression array

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

organism: Schizosaccharomyces pombe

manufacture_protocol: Custom 60mer oligonucleotide microarrays based upon Agilent’s non-contact in situ synthesis process.


title: MPIIB Exiqon mirCURY

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

manufacture_protocol: Locked nucleic acids (LNA) modified microarray capture probes (miRCURY Probe Set, Prod. No. 208010V8.1) were supplied at 480 pmol (Exiqon A/S, Vedbaek, Denmark). Independent of supplier, probes were suspended at a final concentration of 100 µM in Nexterion spot2 buffer (Schott AG, Mainz, Germany) and printed by a BioRobotics MicroGrid II robot (Genomic Solutions Ltd., Huntingdon, UK) onto glass slides coated with poly-L-lysine at 50-55% humidity and room temperature using MicroSpot 2500 quill pins (Genomic Solutions Ltd.). Each slide contained 4 identical replicates with 4 subgrids, respectively. Capture probes were crosslinked to the support by UV irradiation with a total energy of 240mJ UV and blocked with succinic anhydride and 1-methyl-2-pyrrolidone in borate buffer (Fluka, Deisendorf, Germany).


title: Lactobacillus plantarum WCFS1 4K clone array v1.0

first: Michiel

last: Wels

manufacture_protocol: clones of a sequencing library used to sequence L. plantarum WCFS1. Each clone was spotted on the array


title: UCSF C. elegans 20K oligo array version 1

city: POHANG

first: SEUNG-JAE

last: LEE

state: GYEONGBUK

address: SAN 31 HYOJA-DONG, NAM-GU

department: LIFE SCEICNE

institute: POHANG UNIVERSITY OF SCIENCE AND TECHNOLOGY

organism: Caenorhabditis elegans

manufacture_protocol: We used oligonucleotide sets for C. elegans. We printed these oligonucleotides at high density on polylysine-coated glass slides, closely adhering to protocols available at http://microarrays.org.


title: ABI Human Genome Survey Microarray v.1

city: Bergen

first: Mads

last: Aarhus

address: Jonas Lies v 65

department: Center for Medical Genetics and Molecular Medicine

country: Norway

institute: Haukeland University Hospital


title: Maize long oligonucleotide arrays 57K, version 1.13 Array A

first: June

last: Simpson-Williamson

description: similar to Platform GPL5439

manufacture_protocol: REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS  1.Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 μM oligonucleotide solution.  2.Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.  3.The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins.  4.Printing conditions:  Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides. The print head Z- velocity is set to a maximum of 10 mm/sec.  5.Bake slides for 2h at 80oC. Store dry and in darkness at RT.  The microarrays are sent out to recipient scientists at this point. Prior to hybridization, these next steps should be followed:  IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS    1.Rehydrate the microarray slide over 50oC water for 5-10 seconds; snap-dry on a 65oC heating block for 5 seconds. Repeat this step 4-6 times, examining the slides under a dissection microscope (or using red reflectance imaging) to verify complete re-hydration of all the spots. If re-hydration is not complete, repeat the process several more times.  2.Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation. We employ a Stratalinker set at an energy level of 180 mJ.    Re-hydration and UV cross linking can be done well in advance before microarray hybridization, and the slides can be stored at room temperature for several months. However we do not recommend storage of washed microarray slides.  3.Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT.  4.Rinse the slides by plunging 10 times into sterile ddH2O.  5.Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking.  6.Spin dry the slides in a centrifuge at 1000 rpm for 2 min.  7.Store the slides in a light-proof box under cool dry conditions.


title: MIT-HRH-Celegans-MAS8

city: Cambridge

first: Ezequiel

last: Alvarez-Saavedra

address: 77 Massachusetts Avenue  Room 68-411

department: Biology

institute: MIT

manufacture_protocol: Microarray probes were oligonucleotides with sequences complementary to microRNAs and other small RNAs. Each probe was modified with a free amino group linked to its 5' terminus through a 6-carbon spacer (IDT) and was printed onto amine-binding slides (CodeLink, Amersham Biosciences). Printing and hybridization were done using the protocols from the slide manufacturer with the following modifications: the oligonucleotide concentration for printing was 20 μM in 150 mM sodium phosphate pH 8.5, and hybridization was at 50°C for 6 h.


title: DNA Damage Signaling Pathway PCR Array Human PAHS-029

city: Urbana

first: Michael

last: Plewa

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

technology: RT-PCR

description: The Human DNA Damage Signaling RT² Profiler™ PCR Array profiles the expression of 84 genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. DNA damage can result in cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to DNA Damage Signaling with this array.

first: Matias

middle: S

last: Attene-Ramos

first: Elizabeth

middle: D

last: Wagner


title: Illumina Genome Analyzer (Schizosaccharomyces pombe)

last: GEO


title: OUHSC Dyer Neisseria gonorrhoeae 2K MPAUT1a520274F

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

organism:
Neisseria gonorrhoeae
Neisseria meningitidis

first: Thomas

last: Ducey

first: Jeremy

last: Zaitshik

first: Joshua

last: Orvis

first: David

last: Dyer

manufacture_protocol: Custom multipathogen array, probe pairs were designed for each gene to consist of 11 probe pairs (22 features) with a perfect match and a single nucleotide mismatch, probe length=25


title: UCSD/Ideker Kluyveromyces lactis 11k v1.0 (13634)

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

organism: Kluyveromyces lactis

manufacture_protocol: see Agilent for details


title: VRI/Bact Salmonella Typhimurium LT2 5.6K v1.0

status: Public on Oct 24 2007

city: Brno

first: Magdalena

last: Crhanova

address: Hudcova 70

department: Bacteriology

country: Czech Republic

institute: Veterinary research institute

organism: Salmonella enterica subsp. enterica

manufacturer: Veterinary Research Institute, Brno, Czech Republic, Institute of Microbiology, Prague, Czech Republic

first: Marek

last: Basler

manufacture_protocol:
Salmonella Genome Array-Ready Oligo SetTM Version 1.0 (Operon)
1. Oligos are provided in 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in water to 40 µM and add 15 µL of 2x Spotting Solution Plus (Telechem) to final concentration 20 µM.
3. Rearray 15 µl from each well into new 384-well polystyrene plate. Use one of the plates for spotting and the second as stock.
4. Seal plates with Corning seals and store at -20°C.
5. Before printing defrost in laboratory temperature.
6. Centrifuge plates at 2000 rpm for 3 minutes.
7. Remove seals immediately before printing.
8. Print in spotter (Cartesian Technologies PixSysTM PA Serier, Version 4.5) using software CloneTrackerTM Version 1.4.
9. After the print run is completed, seal plates with Corning seals and store at -20°C.
10. Incubate the printed slides at 75% relative humidity overnight for maximum DNA immobilization.
11. Store immobilized microarray slides in the dark and dry.


title: UCSD/Ideker Candida glabrata 11k v1.0 (13566)

organism: Nakaseomyces glabratus


title: JCVI / PFGRC Salmonella Typhimurium/Typhi Version 5

city: Bozeman

first: Stewart

last: Clark

state: MT

address: 366 EPS Building

institute: Center for Biofilm Engineering

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Salmonella enterica subsp. enterica serovar Typhi str. CT18

manufacture_protocol:
Microarray Version : 5
Number of Grids : 48
Element Type : 70mer Oligonucleotide
Surface Coating : Aminosilane
Oligonucleotides Designed : 5462
Replicate Oligo Printings : 4x
Controls : 500 Arabidopsis thaliana 70mers, 10 Arabidopsis thaliana amplicons


title: Paramecium bursaria Chlorella Virus-1 (PBCV-1) oligo array, v.1.2

status: Public on Jan 10 2010

city: Lincoln

first: James

last: Van Etten

state: NE

address: 4240 Fair Street

department: Plant Pathology

institute: University of Nebraska-Lincoln

organism: Paramecium bursaria Chlorella virus 1

description:
This chip  (v.1.2) is similar to the v.1.0 used for the PBCV-1 time course analysis, however, because of a problem during probe printing a few spots were out of place. This problem forced us to create a new annotation file. Thus, we decided to generate a new platform for it to avoid confusion. Chip v.1.2 was mainly used to the aphidicolin treatment experiments.
The Platform data table reflects a condensed representation of the array's replicate features.

manufacturer: DNA Microarray Core Facility, University of Nebraska Medical Center

first: Giane

last: Yanai-Balser

first: Garry

last: Duncan

middle: V

last: Etten

last: Eudy

last: Dunigan

manufacture_protocol: 50-mer probes representing each major PBCV-1 protein encoding gene (CDS) were designed and synthesized by MWG Biotech (Ebersberg, Germany) (20-80% GC, 60-80º C melting temperature).  Probes were spotted onto CMT-GAPS silane-coated slides (Corning, Lowell, MA) using Omnigrid 100 (Genomic Solutions, Ann Arbor, MI) according to manufacturer’s instructions.  Probes were printed in quadruplicates on every slide.


title: Anopheles gambiae transcripts (Vectorbase genebuild AgamP3.4)

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

institute: University of Oxford

organism: Anopheles gambiae

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


title: Dunaliella sp. 0.8 Kb cDNA microarray platform

city: Seoul

first: MinJung

last: Kim

address: 17 Haengdang-dong, Seongdong-gu

department: Life Science

institute: Hanyang University

organism: Dunaliella salina

first: EonSeon

last: Jin

manufacture_protocol: We constructed the cDNA microarrays from the Dunaliella sp. cDNA library (Park et al., 2006). 1052 selected expressed sequence tags (ESTs) from each clone, including housekeeping genes like ribosomal binding proteins, were amplified by PCR using M13 primers and recovered by a MultiScreen PCR Filter Plate (Millipore, Billerica, MA, USA). Each cDNA chip was designed with 778 successfully amplified PCR products from the cDNA library. Additionally, several control clones from the Saccharomyces cerevisiae intergeneic sequence and the Dunaliella sp. housekeeping genes were included. Microarrays were produced using a fully automated system by robotic operation at Digital Genomics (Seoul, South Korea). The cDNA PCR products were spotted onto amine-coated GAPSII slides (Corning Inc., Corning, NY, USA) using MG II (Biorobotics Inc., Woburn, MA, USA) with a 240 um pitch between spots as a twin format. There were 14 x 15 spots per block, and the spot diameter was 100~140 um. To evaluate fabrication, a cDNA microarray was stained with Syto61 (Molecular Probes, Eugene, OR, USA).


title: JHU WEI Mouse MEEBO 35K oligo array

city: Baltimore

first: Laszlo

last: Hackler

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

manufacturer: Johns Hopkins University, Wilmer Eye Institute, Donald Zack`s Laboratory

manufacture_protocol: The Oligator MEEBO 70mer oligonucleotide probe set was printed on ULTRAGAPS slides with a BioRobotics MGII arrayer (4x12 print tool). Probes were dissolved in Full Moon BioSystems`s Print buffer at 10pmol/ul concentration.


title: MPIIB Exiqon Human/Mouse/Rat 16K mirCURY pre-release

first: Hans-Joachim

last: Mollenkopf

manufacture_protocol: Locked nucleic acids (LNA) modified microarray capture probes (miRCURY Probe Set, Prod. No. pre-release) were supplied at 480 pmol (Exiqon A/S, Vedbaek, Denmark). Independent of supplier, probes were suspended at a final concentration of 100 µM in Nexterion spot2 buffer (Schott AG, Mainz, Germany) and printed by a BioRobotics MicroGrid II robot (Genomic Solutions Ltd., Huntingdon, UK) onto glass slides coated with poly-L-lysine at 50-55% humidity and room temperature using MicroSpot 2500 quill pins (Genomic Solutions Ltd.). Each slide contained 4 identical replicates with 4 subgrids, respectively. Capture probes were crosslinked to the support by UV irradiation with a total energy of 240mJ UV and blocked with succinic anhydride and 1-methyl-2-pyrrolidone in borate buffer (Fluka, Deisendorf, Germany).


title: Acidobacteria 42K phylochip

city: Auburn

first: Mark

middle: R

last: Liles

state: AL

address: Rm 316, Rouse Life Sciences Building

department: Biological Sciences

institute: Auburn University

organism: Acidobacteriota

description: The data table contains 42K identifiers for 42K x 3 (triplicate probes) on the array. NGD and POS files lost due to a computer crash.

first: Ozgur

last: Turkmen

first: Brian

middle: F

last: Manske

first: Mingzi

last: Zhang

first: Jean-Marie

last: Rouillard

first: Teri

last: Balser

first: Nedret

last: Billor

first: Robert

last: Goodman

manufacture_protocol: Custom in situ oligonucleotide synthesis using maskless photolithography


title: MPIIB Ambion mirVana

manufacture_protocol: Probes for 200 miRNA (mirVANA Probe Set, lot 124K02) were obtained at 500 pmol each as a collection of amine-modified DNA oligonucleotides targeting a comprehensive selection of human, mouse, and rat miRNAs (Ambion Europe Ltd., Huntingdon, UK). The probes were 42–46 nucleotides (nt) long consisting of a spacer and 18–24 nt specific miRNA segments. They were suspended at a final concentration of 100 µM in Nexterion spot2 buffer (Schott AG, Mainz, Germany) and printed by a BioRobotics MicroGrid II robot (Genomic Solutions Ltd., Huntingdon, UK) onto glass slides coated with poly-L-lysine  at 50-55% humidity and room temperature using MicroSpot 2500 quill pins (Genomic Solutions Ltd.). Each slide contained 4 identical replicates with 4 subgrids. Oligonucleotides were crosslinked to the support by UV irradiation with a total energy of 240mJ UV and blocked with succinic anhydride and 1-methyl-2-pyrrolidone in borate buffer (Fluka, Deisendorf,


title: Legionella pneumophila 0.1K predicted small RNA

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

manufacturer: Howard Shuman Laboratory, Columbia University Medica School

middle: P

first: Gilgi

last: Friedlander

first: Jonathan

last: Livny

first: Hanah

last: Margalit

first: Howard

last: Shuman

manufacture_protocol: Probes were designed for the detection of 101 predicted small RNAs of Legionella pneumophila by using OligiWiz version 2.1.3. The prokaryotic setting was used to design 50-mers probes located, when possible, at the 3’ end of the predicted small RNA. Probes for 10 negative controls, representing 10 genes of the L. pneumophila Paris plasmid, were also designed. Probes (Illumina) were dissolved in 50% DMSO to a final concentration of 30 uM and printed in triplicate on UltraGAPS coated glass slides (Corning) using a PerkinElmer SpotArray microarray printer.


title: Mycobacterium tuberculosis H37Rv custom 44K array

organism: Mycobacterium tuberculosis H37Rv

manufacture_protocol: in-situ synthesis


title: Paramecium bursaria Chlorella Virus-1 (PBCV-1) oligo array, v.1.0

first: James

last: Van Etten

first: Giane

last: Yanai-Balser

first: Garry

last: Duncan

last: Etten

last: Eudy

first: David

last: Dunigan


title: DKFZ SC123 / Operon Human 38k V4.0b - r1

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

organism: Homo sapiens

description:
Spotted long oligonucleotide array, produced using the Operon Human Genome Array-Ready Oligo Set AROS Version 4.0 (35,035 70mer oligonucleotides and additional 764 10p and 22q specific oligonucleotides).
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon

manufacturer: Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany

first: Toedt

last: Grischa

first: Lichter

last: Peter

manufacture_protocol: 70mer oligonucleotides were diluted in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted on epoxy-silane coated glass slides (Schott Nexterion) with stainless steel split pins (SMP3, Telechem) at 20C and 40perc. rH. Slides were dried (1 hr at 60C) and DNA was UV-crosslinked with 240 mJ/cm2 at 254 nm. Slides were stored, sealed airtight and dry, at 4C.


title: DKFZ SC102 / Operon Human 38k V4.0 - r1


title: Affymetrix custom Mayetiola destructor expression array design #SQ237072

status: Public on Oct 06 2009

city: Manhattan

first: Ming

last: Chen

state: KS

address: Kansas State University, 123 Waters Hall

department: Entomology

institute: Kansas State University

organism: Mayetiola destructor

description: Affymetrix custom expression array design #SQ237072. This microarray contains probes designed from transcripts isolated from Hessian fly larval salivary glands and gut.

manufacture_protocol:
1. Arrays were designed by Affymetrix
2. Custom gene expression arrays were generated by Affymetrix using their standard platform


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (MBNI v11 Entrez Gene ID CDF)

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

manufacture_protocol: see the Affymetrix website