title: Universidad Nacional de Rosario Zea Mays 43K

status: Public on Dec 31 2008

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

organism: Zea mays

technology: in situ oligonucleotide

distribution: custom-commercial

first: Virginia

last: Walbot

manufacture_protocol: See http://www.home.agilent.com


title: HPCGG mouse 19k Compugen v1.0

city: Lincoln

first: preston

middle: w

last: estep

state: MA

address: PO Box 53

country: USA

institute: Longenity Inc.

organism: Mus musculus

technology: spotted oligonucleotide

manufacturer: Harvard Medical School - Partners Center for Genetics and Genomics (HPCGG)/Compugen/Sigma-Genosys

first: Preston

middle: W

last: Estep

first: Jason

middle: B

last: Warner

first: Martha

middle: L

last: Bulyk

manufacture_protocol: Compugen/Sigma-Genosys oligonucleotide library spotted onto Corning UltraGAPS slides by Harvard Partners Center for Genetics and Genomics.


title: China Agricultural University Zea Mays 32K Version A

city: Beijing

first: Guohua

last: Mi

address: Yuan-Ming-Yuan West Rd 2

department: Plant Nutrition

country: China

institute: China Agricultural University

distribution: non-commercial

manufacturer: Arizona University,Maize Oligonucleotide Array Project

first: Jack

last: Gardiner

manufacture_protocol:
http://www.maizearray.org
Spotted oligo array on glass. The whole maize array set similar to 1.1 version contains 55550 unique probes from maize and array A contains 28833 of them. The number of total spots including empty and controls is 32448.


title: Custom Agilent peanut oligonucleotide microarray (8 x 15k)

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

organism: Arachis hypogaea

description: 8 x 15k arrays

first: Paxton

last: Payton

first: KameswaraRao

manufacture_protocol: In situ-oligonucleotide synthesis


title: National Cancer Center of Singapore Human 32k BAC array(B) version 1

status: Public on Dec 29 2008

city: Singapore

first: Wu

last: Yonghui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Center of Singapore

organism: Homo sapiens

technology: spotted DNA/cDNA

description: This platform includes 15621 BAC clones, amplified by DOP-PCR, selected by fingerprint mapping to cover the entire human genome in a tiling fashion.

manufacture_protocol: as described in MFN manual


title: University of Goettingen Ambion miRNA array version 1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

manufacturer: DNA Microarray Facility, University of Goettingen

first: Reiner

last: Hitt

first: Dirk

last: Motzkus

manufacture_protocol:
- Ambion mirVana probe library spotted on Amine-Binding Slides (Amersham CodeLink) with Biorad Chipwriter Pro
- Printing conditions:
Single array element printed per oligonucleotide, 6 pins in the print head, 50% relative humidity
- hydratize slides for 24h


title: DSBB Maize 1k v.1.0

status: Public on Dec 22 2008

city: Milano

first: Rosanna

last: Marino

state: Milano

address: Via celoria 26

department: Department of biomolecular sciences and biothecnology

country: Italy

institute: Universita' degli studi di Milano

manufacture_protocol: MWG microarrays are made by spotting 50-mer oligonucleotides onto epoxy treated glass slides. For more details see manufacturer's web site


title: China Agricultural University Zea Mays 32K Version B


title: CHUV_CIG_Trichophyton rubrum_10K_V1

city: Lausanne

first: Michel

last: Monod

address: Av. de Beaumont 29

department: Dermatology

country: Switzerland

organism: Trichophyton rubrum

description: The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacturer: DNA Array Facility, Center for Integrative Genomics, Genopode, University of Lausanne; Centre Hospitalier Universitaire Vaudois, Dermatology department, mycology laboratory

manufacture_protocol: The Trichophyton rubrum array contains ~2300 unique PCR products from an EST library derived from T. rubrum grown on protein media. The spotting buffer is 3xSSC 1,5M betaine, the spotting robot is a GeneMachines OmniGrid300. DNA was spotted on aldehyde slides.


title: Axtell_Physco_rdr6_Linker3 (Solexa sequencing)

status: Public on Dec 19 2008

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

organism: Physcomitrium patens

technology: other

description: Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This platform is all small RNA sequences from two technical replicates from 10 day old rdr6-19 plants.  See Cho et al. for details.

distribution: virtual

first: Sung-Hyun

last: Cho

first: Charles

last: Addo-Quaye

first: Ceyda

last: Coruh

first: Asif

last: Arif

first: Wolfgang

last: Frank

first: Zhaorong

last: Ma


title: National Cancer Center of Singapore Human 32k BAC array(A) version 1

description: This platform includes 16829 BAC clones, amplified by DOP-PCR, selected by fingerprint mapping to cover the entire human genome in a tiling fashion.


title: GGSIU Agilent Rice Array 22K

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

organism: Oryza sativa

first: Ravi

middle: R

last: Pathak

manufacture_protocol: 60-Oilgomer Format


title: Arabidopsis Genome Array-Ready Oligonucleotide Microarray V3.0.3

organism: Arabidopsis thaliana

distribution: commercial

manufacturer: The Galbraith Lab, University of Arizona

first: Priyanka

last: Shrarma

first: Beena

last: Pillai

manufacture_protocol: 29,000 element Arabidopsis Oligonucleotide Microarrays, using the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0.


title: IMS human 0.6K v.1

city: Minato-ku

first: Naoyuki

last: Takahashi

state: Tokyo

address: 4-6-1, Shirokanedai

department: Research Hospital

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Probes for 200 target genes were spotted singly in the first and second block and those for 195 target genes in the third block.  Probes for 8 positive and 4 negative control genes were spotted doubly in every block.  It was confirmed that each spot contained the same amount of probes throughout the three thin chips which were set into a holder together.

first: Noriharu

last: Sato

first: Tatsunobu

last: Fukushima

first: Arinobu

last: Tojo

first: Satoshi

manufacture_protocol:
In this study, we used a custom-made fibrous oligonucleotide DNA microarray Genopal (Mitsubishi Rayon) for 595 target genes, which were selected from genes encoding cytokines, cytokine receptors, chemokines, chemokine receptors, adhesion molecules, and signal transducers, as well as for 8 positive control genes (GAPDH, ACTB, RPS5, K-ALPHA-1/TUBA1B, ATP5F1, GTF2B, PLA2G5, and TFRC)ã~@~@and 4 negative control genes (lambda A, lambda B, Omp A1, and Omp A2).
All oligonucleotide capture probes (70 mer in length), including those for positive and negative controls, were designed to have approximately the same annealing temperature (Tm)ã~@~@throughout a microarray.  In addition, each probe was designed also to hybridize to its target antisense RNA specifically within 1 kb from 3â~@~Y-end.
The custom-made fibrous oligonucleotide DNA microarray, Genopal (Mitsubishi Rayon), was manufactured in the following manner.  Hollow plastic fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel, were bundled in an orderly arrangement, hardened with resin to form a block (12 rows Ã~W 19 columns) and then sliced into thin chips.  Finally, three thin chips were set into a holder together.


title: IMS human 0.6K v.2

description: Probes for 207 target genes were spotted singly in the first block, those for 205 target genes in the second block, and those for 203 target genes in the third block.  Probes for 8 positive and 4 negative control genes were spotted singly in every block.  It was confirmed that each spot contained the same amount of probes throughout the three thin chips which were set into a holder together.

manufacture_protocol:
In this study, we used a custom-made fibrous oligonucleotide DNA microarray Genopal (Mitsubishi Rayon) for 615 target genes, which were selected from genes encoding cytokines, cytokine receptors, chemokines, chemokine receptors, adhesion molecules, and signal transducers, as well as for 8 positive control genes (GAPDH, ACTB, RPS5, K-ALPHA-1/TUBA1B, ATP5F1, GTF2B, PLA2G5, and TFRC)　and 4 negative control genes (lambda A, lambda B, Omp A1, and Omp A2).
All oligonucleotide capture probes (70 mer in length), including those for positive and negative controls, were designed to have approximately the same annealing temperature (Tm)　throughout a microarray.  In addition, each probe was designed also to hybridize to its target antisense RNA specifically within 1 kb from 3’-end.
The custom-made fibrous oligonucleotide DNA microarray, Genopal (Mitsubishi Rayon), was manufactured in the following manner.  Hollow plastic fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel, were bundled in an orderly arrangement, hardened with resin to form a block (12 rows × 19 columns) and then sliced into thin chips.  Finally, three thin chips were set into a holder together.


title: CapitalBio Mammalian miRNA Array Services V1[1].0

city: Shanghai

first: JIANREN

last: GU

address: No.25/Ln.2200, Xietu Road,

department: State Key Laboratory of Oncogenes and Related Genes

institute: Shanghai Cancer Institute, Shanghai Jiao Tong University

manufacture_protocol: The limited sequence length of miRNAs leaves little consideration for probe design strategy; all miRNA probe sequences were designed to be complementary to the full-length mature miRNA. To facilitate probe immobilization on aldelhyde modified glass (CapitalBio Corp., Beijing, China), the probe sequences were concatenated up to 40 nt and modified with 5′-amino-modifier C6 oligonucleotide. In addition, we designed 8 short oligos with no homology to existing RNA sequences to serve as negative controls; the corresponding synthetic miRNAs were generated by in vitro transcription using Ambion's miRNA Probe Construction Kit (Ambion, Austin, TX). Various amounts of synthetic miRNAs were spiked into the interrogated RNA samples.


title: Axtell_Physco_dcl3_Linker2 (Solexa sequencing)

first: Michael

description: Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This platform is all small RNA sequences from 10 day old dcl3 samples (line 5 and 10).  See Cho et al. for details.


title: Beijing Institute of Biotechnology NimbleGen Shigella flexneri 12K array

first: Li

last: Zhu

address: 20 Dongdajie, Fengtai District

department: State Key Laboratory of Pathogens and Biosecurity

institute: Beijing Institute of Biotechnology

organism: Shigella flexneri 2a str. 2457T

description: Maskless Array Synthesizer (MAS) technology

manufacture_protocol: Available at manufacturer's website: www.nimblegen.com


title: Custom Agilent peanut oligonucleotide microarray (4 x 44k)

first: Kameswara Rao

last: Kottapalli

description: 4 x 44k arrays (22k replicated)

first: Paxton

last: Payton

first: KameswaraRao


title: Lactococcus lactis pangenome 385K short oligo array

city: Nijmegen

first: Jumamurat

last: Bayjanov

address: Geert-Groteplein

country: Netherlands

institute: CMBI

organism: Lactococcus lactis

description:
All genomic, plasmid and single gene or operon DNA sequences (1988 sequences in July 2005, constituting 10.7 Mb) of L. lactis were collected from the NCBI CoreNucleotide database and were deposited in a local database. This included complete genome sequences of L. lactis strain IL1403 (2.35 Mb, accession number AE005176) and fragments of the genome of strain SK11 (2.43 Mb, Genbank record GI:62464763). Additionally, draft genome sequences consisting of 547 contigs (2.3 Mb) of L. lactis ssp. lactis strain KF147 (NIZOB2230) and 961 contigs (2.6 Mb) of L. lactis ssp. lactis KF282 (NIZOB2244W) were added to this database. Redundant stretches of DNA were removed from the database, where a stretch of DNA was defined as redundant if it differed from another piece of DNA by at most 2 nucleotides over a window of 100 nucleotides. For the remaining non-redundant 7 Mb of DNA, a 32-mer tiling design was defined by starting an oligomer approximately every 19 nucleotides, resulting in a total of 386,298 probes. We also designed 3181 random probes with their sequence absent in the non-redundant 7 Mb of DNA and they were randomly located on the array.
Probes target mainly L. lactis ssp. lactis IL1403 public genome and then incomplete genome of L. lactis ssp. cremoris SK11 (now it is completed). Recently, closely related genome of strain L. lactis ssp. cremoris MG1363 has been published. All these 3 genomes are publicly available at NCBI databases.
Since there is no reference strain the probes target DNA from different strains, hence, there is no positions file (*.pos). The .ndf file is linked below as a supplementary file.

manufacturer: NimbleGen Systems Inc. (Madison, WI, USA)

first: Douwe

last: Molenaar


title: NCHU_M&A_human  1152 cDNACHIP

city: Taichung

first: Chen-Yu

last: Lee

address: 250, Kuo Kuang Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

manufacturer: National Chung Hsing University,College of Life Sciences,The Graduate Institute of Biomedical Sciences (GIBMS)

first: Cheng-Yu

first: Hui-Fang

last: Sher

first: Pan-Chyr

last: Yang

first: JJW

last: Chen

manufacture_protocol: We obtained 1,152 human EST clones with putative gene names related to cell adhesion, motility, angiogenesis, signal transduction, tumorigenesis, and metastasis, etc. (Chen JJ, Peck K, Hong TM etc. Global analysis of gene expression in invasion by a lung cancer model. Cancer Res 61:5223-5230, 2001) from the IMAGE consortium libraries through its distributor (Research Genetics, Huntsville, AL). Three copies of 1,152 PCR-amplified cDNA fragments were prepared by arraying machine built in house and spotted per microarray membrane (measuring 18 X 27 mm). The whole system included tool pin, adapter, washing slots, sampling slots, sample distribution region, program and automatically changing plate system. Those treated pins were fitted into multiple-pore adapter, which is designed specially to make the pins elastic while spotting samples on membrane. The adapter could be changed for single or multiple pins system according to experimental need. The PCR-amplified cDNA in V-bottomed 96-well microtiter plates were distributed onto a positively charged nylon membrane with spots spaced 150 um apart by an arraying machine. The arraying machine was a computer controlled XYZ translation system outfitted with Teflon-coated tool pins for sample delivery. It was designed and constructed by Wittech company (Taipei, Taiwan) with position resolution and repeatability better than ± 5 um. Samples were held at the tip of the pins for delivery by the action of surface tension, and the delivery volume was governed by the diameter of the tips. Every time after DNA was spotted on membranes, by means of movement of translation stage, the solid pin was immersed into washing slots, and washed by 95% ethanol, and deionized water respectively with sonicating.


title: CRCNA_human_gdA2322

status: Public on Dec 20 2008

city: Nantes

first: Emmanuel

last: Scotet

address: 9 quai moncousu

country: France

institute: INSERM

first: Aurélie

last: Thedrez

first: Marc

last: Bonneville

manufacture_protocol: PIQOR Immunology


title: SIBS hmr microRNA microarray v2.0

city: shanghai

first: huang

last: bing

state: shanghai

address: yueyang road 320

department: chemistry

institute: Chinese Academy of Sciences

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: epoxide coated slide made in our lab

first: Zhao

last: botao

first: Liang

last: Ruqiang

first: Ruan

last: kangcheng

first: Jin

last: youyin

manufacture_protocol: Antisense probes of microRNAs and small RNAs were spotted at 20 uM on epoxide slides. Labeled PCR products from small RNA libraries were hybridized for 16h at 45°C in 4XSSC,0.1% SDS.


title: Axtell_Physco_WT_Linker1 (Solexa sequencing)

first: Michael

last: Axtell

description: Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker and the linkers removed.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This platform is all retained small RNA sequences from two technical replicates from 10 day old Wild-Type.  See Cho et al. for details.

first: Sung-Hyun

last: Cho

first: Charles

last: Addo-Quaye

first: Ceyda

last: Coruh

first: Asif

last: Arif

first: Wolfgang

last: Frank

first: Zhaorong

last: Ma


title: University of Lausanne Mouse 17K (M17K) array version 1

status: Public on Dec 15 2008

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

institute: University of Lausanne

manufacturer: DAFL (DNA Array Facility of the University of Lausanne)

manufacture_protocol: The M17K chip is made using the 15'000 gene clone set (NIA 15k cDNA set) available from the National Institute on Aging. These cDNA clones are derived from embryonic and fetal mouse tissues. An additional 1400 cDNA clones have been added from genes not not contained in the NIA collection. The cDNA are spotted onto glass slide with a GeneMachines OmniGrid300 spotting robot.


title: SIBS hmr microRNA microarray v1.0


title: Drosophila_Melanogaster_NCSU_ARRAY

status: Public on Dec 17 2008

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

organism: Drosophila melanogaster

description: We constructed the cDNA microarrays using 4,256 expressed sequence tags (ESTs) from a library sequenced by the Berkeley Drosophila Genome Project (BDGP) and provided by Research Genetics, which were reamplified by  PCR in 96-well format in the Genome Research Laboratory at North Carolina State University. We transferred clones that showed a strong, single band to 384-well plate format, and spotted the DNA onto ArrayIt SuperAmine slides (Telechem) at a spacing of 225 m using an Affymetrix 417 Arrayer with the Pin and Ring method25 (Genetic Microsystems) that results in relatively uniform DNA deposition within 125 m diameter spots. We then cross-linked the DNA to the slides with 1,200 J of irradiation in a UV Stratalinker (Stratagene) and processed the slides according to the manufacturer's recommendations

manufacture_protocol: Clones were spotted onto ArrayIt SuperAmine slides (Telechem) at a spacing of 225 nm using an Affymetrix 417 Arrayer with the Pin and Ring method25 (Genetic Microsystems) that results in relatively uniform DNA deposition within 125 m diameter spots.


title: Listeria monocytogenes strain F2365 5.6K

city: Wyndmoor

first: yanhong

last: Liu

address: 600 E. Mermaid Lane

institute: ERRS-ARS-USDA

organism: Listeria monocytogenes

first: Yanhong

first: Amy

last: Ream

manufacture_protocol:
The custom oligonucleotide microarray is synthesized on a semiconductor using an electrochemical synthesis process. Each oligonucleotide probe (spot) is synthesized on a platinum electrode that is independently controlled by the synthesizer’s computer. Synthesis is based on established phosphoramidite chemistry and occurs at thousands of sites simultaneously according to a computer algorithm that activates only specified electrodes. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are not involved in the process, all probes can be easily changed without extra time or cost.
The oligonucleotides are synthesized in a proprietary porous reaction layer that coats the surface of the semiconductor, and acts to covalently attach the oligonucleotide to the surface of the chip.


title: IMB-Mattick Mouse 4k 5

status: Public on Dec 12 2008

city: Brisbane

first: Larry

last: Croft

state: QLD

address: The University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

first: Ryan

last: Taft

first: Marjan

last: Askarian Amiri

first: Xiaochuan

last: Zhou

first: Cas

last: Simons

first: John

middle: S

last: Mattick

manufacture_protocol: Small RNA probes were designed in the IMB by Larry Croft. LNA-modified RNA probes were synthesized in situ at LCSciences using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip. See the LC Sciences web page for additional details.


title: JCVI-PFGRC Listeria monocytogenes array version 2

status: Public on Dec 25 2008

city: Normal

first: Arunachalam Muthaiyan

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

state: IL

address: Julian Hall

institute: Illinois State University

description:
This set includes 6347 oligonucleotides distributed in 48 grids.
This is condensed template of replicated features of JCVI/PFGRC/TIGR Listeria monocytogenes version 2 array. For full template information please refer: http://pfgrc.jcvi.org/index.php/microarray/array_description/listeria_monocytogenes/version2.html

manufacture_protocol: Number of Grids - 48; Element Type - 70mer Oligonucleotide; Surface Coating - Epoxy; Oligonucleotides Designed - 6347; Replicate Oligo Printings - 4x; Controls- 480 Arabidopsis thaliana 70mers.


title: IMB-Mattick Mouse 4k 1


title: IMB-Mattick Human 4k 23

first: L

first: R

first: M

first: X

first: C

first: J


title: IMB-Mattick Mouse 4k 4


title: Agilent Mouse Developmental Custom Microarray 44K (RIKEN-BioResurce +MPI-MolecularBiomedicine)

status: Public on Dec 30 2008

city: Muenster

first: Marcos

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

first: Guangming

last: Wu

first: Luca

last: Gentile

first: Jeong

last: Tae Do

first: Tobias

last: Cantz

first: Julien

last: Sutter

first: Katherina

last: Psathaki

first: Telma

last: Esteves

last: Arauzo-Bravo

first: Claudia

last: Ortmeier

first: Takuya

last: Fuchikami

first: Kuniya

last: Abe

first: Hans

last: Scholer

manufacture_protocol: see manufacturer's web site


title: Boophilus microplus EST microarray (NimbleGen)

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

organism: Rhipicephalus microplus


title: IMB-Mattick Mouse 4k 3

first: Larry

last: Croft

first: Ryan

last: Taft

first: Marjan

last: Askarian Amiri

first: Xiaochuan

last: Zhou

first: Cas

first: John


title: Agilent 95k Human Promoter v1 013590

city: Cambridge

first: Garrett

middle: M

last: Frampton

address: 9 Cambridge Center

institute: Whitehead Instute - MIT

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


title: IMB-Mattick Mouse 4k 20

first: L

first: R

first: M

first: X

first: C

last: Simons

first: J

last: Mattick


title: IMB-Mattick Mouse 4k 17


title: Washington University Saccharomyces 70 mer 13K oligonucleotide microarray v1

city: Dallas

first: Hyun Seok

last: Kim

address: Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism: Saccharomyces cerevisiae

manufacturer: Microarray core at Washington University's Genome Center

first: Barak

middle: A

last: Cohen

manufacture_protocol: 6388, 70mer oligos (Qiagen-Operon, USA) were spotted onto epoxy-coated slides (MWG Biotech, USA) in duplication.


title: NHLBI-Mouse-Solexa-Tcell-Stat

status: Public on Dec 11 2008

city: Bethesda

first: Dustin

middle: E

last: Schones

state: MD

address: Building 10, Room 7B20A, 9000 Rockville Pike

institute: NHLBI/NIH


title: StanfordGenetics/SherlockLab-Scerevisiae-SolexaRNASeq-PolyA RNA

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description:
Solexa Sequencing
Solexa Genome Analyzer (GA1)


title: Long oligo 44K tracking array

status: Public on Dec 18 2008

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

organism:
Saccharomyces cerevisiae
Homo sapiens
Mus musculus
synthetic construct

first: Timothy

last: Hughes

first: Eran

last: Segal

first: Jonathan

last: Widom

manufacture_protocol: Agilent SurePrint Technology


title: Acropora millepora_13KcDNA_v1.0

status: Public on Dec 05 2008

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

institute: Australian National University

organism: Acropora millepora

manufacturer: Adelaide Microarray Facility, University of Adelaide, Adelaide, Australia

manufacture_protocol: Microarrays were generated by spotting amplified cDNA onto GAPSII slides using a Biorad Chipwriter Pro, and then fixed by a combination of UV light exposure (150 mJ) followed by baking at 80°C for 3 hours.


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 11, Hs133Av2_Hs_ENTREZG]

status: Public on Dec 10 2008

city: Firenze

first: Luca

last: Beltrame

address: Viale Pieraccini 6

department: Department of Pharmacology

institute: University of Firenze

description: This is identical to GPL571 but a custom CDF environment was used to extract data [Brainarray Version 11, Hs133Av2_Hs_ENTREZG].

relation: Alternative to: GPL571 (Alternative CDF [official])

manufacture_protocol: Affymetrix standard protocol


title: CEA - DSV/IRCM/LEFG : NIA Version 2

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

first: Amelie

last: Robert

first: Peggy

last: Maltere

first: Franck

last: Amiot

manufacture_protocol: The mouse chip consists of a large set of 13440 cDNA clones from early mouse embryo libraries constructed by the National Institute of Aging (NIA) (http://www.nia.nih.gov) representing about 11 000 genes.    It also includes positive (actin, tubulin, oligodT, cot-1 DNA) and negative (TE/DMSO) controls (384 probes) present many times in the array for quality control.


title: CEA - DSV/IRCM/LEFG : NIA Version 1

manufacture_protocol: The mouse chip consists of a large set of 13056 cDNA clones from early mouse embryo libraries constructed by the National Institute of Aging (NIA) (http://www.nia.nih.gov) representing about 11 000 genes. An additional set of 384 cDNA clones consisting essentially in IMAGE clones.    It also includes positive (actin, tubulin, oligodT, cot-1 DNA) and negative (TE/DMSO) controls (384 probes) present many times in the array for quality control.


title: IMB-Mattick Mouse 4k 6

first: Larry

last: Croft

first: Ryan

last: Taft

first: Marjan

last: Askarian Amiri

first: Xiaochuan

last: Zhou

first: Cas

first: John


title: JHMI/Zhu_YEAST_14K_v1.0

city: Baltimore

first: Eitan

last: Halper-Stromberg

address: 733 N Broadway

institute: Johns Hopkins

technology: spotted peptide or protein

first: Heng

last: Zhu

manufacture_protocol:
We have constructed a yeast proteome microarray containing approximately 80% yeast proteins and screened it for a number of biochemical activities. We first built a high-quality collection of 5800 yeast open reading frames (ORFs) (93.5% of the total) cloned into a yeast high-copy expression vector using recombination cloning. The yeast proteins are fused to glutathione S-transferase-polyhistidine (GST-HisX6) at their NH2-termini and expressed in yeast using the inducible GAL1 promoter. The yeast expression strains contain individual plasmids in which the correct yeast ORFs have been shown to be fused in-frame to GST by DNA sequencing. The proteins were expressed in yeast to help ensure that the proteins were modified and folded properly. Using a 96-well format, 1152 samples were purified at once from yeast extracts using glutathione-agarose beads. We included 0.1% Triton in the lysis buffer and washes to ensure that the purified proteins were free of lipids. The quality and quantity of the purified proteins were monitored using immunoblot analysis of 60 random samples. Greater than 80% of the strains produced detectable amounts of fusion proteins of the expected molecular weight.
To prepare the proteome chips, we printed 6566 protein preparations, representing 5800 different yeast proteins, in duplicate onto glass slides using a commercially available microarrayer. Our initial experiments used aldehyde-treated microscope slides in which fusion proteins attach to the surface through primary amines at their NH2-termini or other residues of the protein. In subsequent experiments, we spotted proteins onto nickel-coated slides, in which the fusion proteins attach through their HisX6 tags and presumably uniformly orient away from the surface. Although both slides were successful, the nickel-coated slides gave superior signals for our particular protein preparations.
To determine how much fusion protein was covalently attached to different glass surfaces and the reproducibility of the protein attachment, we probed the chips with antibodies to GST (anti-GST). More than 93.5% of the protein samples gave signals significantly above background (i.e., greater than 10 fg of protein), and 90% of the spots contained 10 to 950 fg of protein. Our results also demonstrate that it is feasible to spot, with excellent resolution, 13,000 protein samples in one-half the area of a standard microscope slide. To test the reproducibility of the protein spotting, we compared the signals from each pair of duplicated spots with one another; 95% of the signals were within 5% of the average.


title: 2007-05-17_C_elegans_ChIP_02

city: Chapel Hill

first: Everett

address: 1000 Manning Dr.

institute: UNC

organism: Caenorhabditis elegans

first: Susan

last: Strome

first: Jason

last: Lieb

manufacture_protocol: Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697


title: NimbleGen 385k S. cerevisiae 32bp tiling array

status: Public on Dec 04 2008

middle: D

address: 203 Fordham Hall

institute: University of North Carolina at Chapel Hill

description: S. cerevisiae whole-genome tiling arrays covering entire genome at 32bp resolution with 50bp probes. 385,000 probes total.


title: Luminex Kinase Phosphorylation Immunosandwich Assay

first: Jinyan

last: Du

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Institute

technology: antibody

manufacturer: The Broad Institute, Cancer Program, Golub Lab

first: Paula

last: Bernasconi

first: Karl

last: Clauser

first: DR

last: Mani

first: Stephen

middle: P

last: Finn

first: Rameen

last: Beroukhim

first: Melissa

last: Burns

first: Bina

last: Julian

first: Xiao

last: Peng

first: Haley

last: Hieronymous

first: Rebecca

last: Maglathin

first: Timothy

last: Lewis

first: Linda

last: Liau

first: Phioanh

last: Nghiemphu

first: Ingo

middle: K

last: Mellinghoff

first: David

middle: N

last: Louis

first: Massimo

last: Loda

first: Steven

last: Carr

first: Andrew

last: Kung

first: Todd

last: Golub

manufacture_protocol:
Individual bead-type of Luminex xMAP microspheres (Luminex Corporation, Austin, TX) were coupled separately to capture antibodies against total tyrosine kinases using the following procedure. 100µl Microspheres were washed with 100 µl ddH2O and resuspended in 80 µl 100mM NaH2PO4 pH 6.2. 10 µl 25mg/ml Sulfo-NHS (Pierce) and 10 µl 25mg/ml EDC (Pierce) were added and incubated at 25°C for 20min while shaking to activate the microspheres. The activated beads were washed with 250 µl 1x PBS pH7.4 twice and resuspended in 200 µl 1x PBS. 20 µg capture antibodies in 50 µl 1x PBS were added. The mixtures were incubated at 25°C  for two hours while shaking in dark. The antibody-coupled beads were blocked with 500 µl PBS-TBN (0.02% Tween-20, 0.1% BSA and 0.05% NaN3 in 1x PBS pH7.4) at 25°C  for 30 minutes while shaking. Finally, the microspheres were washed with 500 µl PBS-TBN twice and stored in 500 µl PBS-TBN at 4°C until use.
0.25 µl coupled microspheres per bead type were used for each sample. Microsphere mixture were transferred into a 96-well 1.2um filter plate (Millipore) and washed with 100 µl 1x PBS-1% BSA pH7.4 (Sigma) twice. 100 µl 1mg/ml protein lysates were added to each well and incubated at 4°C overnight while shaking. The microspheres were washed with 100µl 1x PBS-1% BSA pH7.4 twice. 50µl 4µg/ml biotin-4G10 (UpState) were added and incubated at 25°C  for 30 minutes while shaking. The microspheres were then washed with 100µl 1x PBS-1% BSA pH7.4 twice and then incubated with 50µl 4µg/ml R-phycoerythrin streptavidin conjugates (Molecular Probes) at 25°C  for 10 minutes. Finally, the samples were washed with 100µl 1x PBS-1% BSA pH7.4 twice and resuspended in 50µl 1x PBS-1% BSA pH7.4 for analysis.
The data were acquired with a Luminex 100 instrument (Luminex Corporation) according to manufacturer’s instructions. The background readings for each capture antibody were obtained using microspheres incubated with 1x cell lysis buffer (Cell Signaling Technology). Values were considered positive if they were 3-fold over the background and represented by log2-transformation of the folds over background. Negative values were threshold to -10. The preprocessed data were converted into .gct files and analyzed with GenePattern 3.0 (The Broad Institute).


title: Adolf Butenandt Institute Drosophila melanogaster 385K Tiling Array version 1

status: Public on Dec 13 2008

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description:
All of chr X, parts of 2L, 2R, 3L and 3R. Based on dm2/FlyBase release 4.3. isothermal probe design, about 1 probe/100 bases.
2006-02-16_Becker_DMEL_ChIP tiling design


title: UNSW_S.cerevisiae_6.5K_v3

status: Public on Dec 01 2008

city: Sydney

first: Bettina

last: Rosche

state: NSW

address: Kensington

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

manufacturer: Ramaciotti Centre for Gene Function Analysis, NSW, Australia

first: Allen

last: Chen

first: Cristy

last: Gelling

first: Peter

last: Rogers

first: Ian

last: Dawes

manufacture_protocol: The Pan Yeast microarray oligonucleotide probe set obtained from MWG Biotech (Germany) was spotted onto Eppendorf (Germany) epoxy-coated microarray substates.  For any queries on the spotting protocol, contact the manufacturers (Ramaciotti Centre for Gene Function Analysis - http://ramaciotti.science.unsw.edu.au)


title: Blanchette/Green Splice Junction array

city: Berkeley

first: Kasper

middle: Daniel

last: Hansen

address: 461 Koshland Hall

department: PMB

institute: UC Berkeley

description:
This array is a splice junction array designed for D . Melanogaster using FlyBase 4. The array encompasses all genes that are annotated as having alternative transcripts. For each transcript, probes targeting alternative junctions and exons awere designed as well as probes targeting some constitutive (but not all) exons and junctions. The array design is very similar (essentially an update) to the design described in Blanchette et al. "Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila" in Genes Dev 2005.
Probes on the array were "t-stilted", that is every probe was extended by a poly T-tail in order to move the probe off the array surface, nucleotide sequences are given with and without stilts.

first: Richard

last: Green

first: Marco

last: Blanchette

manufacture_protocol: Standard Agilent


title: IMB-Mattick Mouse 4k 2

first: Larry

last: Croft

address: The University of Queensland, St Lucia

institute: Institute for Molecular Bioscience

organism: Mus musculus

first: Ryan

last: Taft

first: Marjan

last: Askarian Amiri

first: Xiaochuan

last: Zhou

first: Cas

last: Simons

first: John

last: Mattick


title: Anopheles gambiae genome array design for Zeitgeber project

status: Public on Nov 13 2008

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Anopheles gambiae

description: Agilent - based oligonucleotide genome array for A. gambiae

manufacture_protocol: Agilent


title: IMB-Mattick Human 4k 10

organism: Homo sapiens


title: IMB-Mattick Mouse 4k 19

first: L

first: R

first: M

first: X

first: C

first: J


title: IMB-Mattick Mouse 4k 18


title: IMB-Mattick Human 4k 22


title: IMB-Mattick Mouse 4k 21


title: Agilent Yeast Oligo Microarray 4x44K G2519F (condensed)

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

description: Platform data table condensed by Agilent Probe Name.


title: Affymetrix Mycobacterium bovis BCG GeneChip Array

city: ft. meade

first: Hyeung-Jin

last: Jang

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

organism: Mycobacterium tuberculosis variant bovis BCG

description:
Version=2
Arrays=M_bovisa520552F
NURLS=1


title: IFTC Saccharomyces cerevisiae 154 v1.0

city: Leipzig

first: Franziska

last: Heine

address: Permoserstraße 15

department: Environmental Microbiology

institute: Helmholtz-Centre for Environmental Research - UFZ

description: The microarray presents 154 oligonucleotides (70mer) in triplicate encoding for selected proteins of the G1- and S-phase from the cell cycle of S. cerevisiae as well as selected oligonucleotides encoding for proteins belonging to the various metabolic pathways, glucose transporters and flocculins of S. cerevisiae.

manufacturer: Working group "Chiptechnology" at the Institute of Technical Chemistry of the Leibniz University of Hanover, Germany

first: Frank

last: Stahl

first: Heike

last: Sträuber

first: Claudia

last: Wiacek

first: Dirk

last: Benndorf

first: Cornelia

last: Repenning

last: Schmidt

first: Thomas

last: Scheper

first: Martin

last: von Bergen

first: Hauke

last: Harms

first: Susann

last: Müller

manufacture_protocol:
Oligonucleotide design and synthesis: Oligonucleotides were designed and synthesised by the manufacture Operon excepting oligonucleotides representing Lg-FLO1. These oligonucleotides were designed using DNA-Star, blasted at NCBI (National Center for Biotechnology Information) and afterwards synthesised by Operon.
Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: Malaria Print 20060818ML_PMC

city: Pretoria

first: Anna

middle: Catharina (Tharina)

last: van Brummelen

state: Gauteng

address: Lynwood Road

department: Biochemistry

country: South Africa

institute: University of Pretoria

organism: Plasmodium falciparum

manufacturer: Princeton University Microarray Facility

manufacture_protocol:
1. Oligos are arrayed in 384-well Genetix polystyrene V-bottom plates (cat# X7020). Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 3X SSC to 40 uM.
3. Lyophilize oligos in Genetix plates by centrifugation in a Savant Speed Vac plate spinner (Model SC210A).
4. Before printing, add 15 µL of water to each well. This can be done the night before a print run is started.
5. Seal plates with parafilm and shake gently overnight at 4C.
7. Centrifuge plates at 2000 rpm for 1 minute immediately prior to loading on the printer.
8. Remove parafilm immediately prior to loading ech plate.
9. Load plate onto platform in order designated, as each round completes
10. Cover completed plate with parafilm and return to 4C.
11. After the print run is completed, Speed Vac plates to dry.
12. For each subsequent preparation of these plates for a print run, add water to the wells. The amount of water should be decreased by 0.5 µL per print run, as this is the amount drawn up by the pin capillary during each print.
poly-lysine glass from Erie Scientific


title: UHN_Human_10K_v1

city: Toronto

first: Zhibin

last: Lu

state: ON

address: 101 College St, TMDT 9-308G

country: Canada

institute: UHN Microarray Centre

description:
Grid rows	12
Grid Columns	4
Rows	14
Columns	16
Grid to Grid distance	4500um
Spot to Spot distance	200um
Spot size	100um

manufacture_protocol:
1. Acquisition of bacterial clone set—These are well characterized human ESTs, and annotations for most clones in this clone set are available in OMIM, RefSeq and/or SwissProt IDs.
2. Clone set is PCR amplified and DNA purified in working 96 well plates.
3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from .10ug/ul to 0.25ug/ul.  These are used for spotting.
4. We use high precision robots that can use up to 48 pins or print heads.   H10k slides are printed using 48 pins and we use UltraGAPS slides (Corning Inc.)  We are able to print up to 120 slides in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests.
5. Post Printing Quality Control tests include: A real hybridization using commercially available RNA; Vector Probe labeling method; Terminal Transferase tailing method.


title: Psychrobacter arcticus 273-4 whole genome oligonucleotide array

city: East Lansing

first: Peter

last: Bergholz

state: MI

address: 540 Plant and Soil Sciences

department: Center for Microbial Ecology

institute: Michigan State University

organism: Psychrobacter arcticus 273-4

first: Monica

last: Ponder

first: Jeff

last: Landgraf

first: James

last: Tiedje

manufacture_protocol: 70-mer oligonucleotide probes were designed and synthesized by Operon Biotechnologies, Inc.  Probes were provided to Michigan State University in 96-well plate format.  Probes were spotted onto Corning Ultra-GAPS II slides in a Genemachines Omnigrid Robot using 8 Telechem Chipmaker pins.  Arrays were spotted in duplicate on slides and allowed to dry under controlled humidity.  Probes were UV-crosslinked to slides Stratagene Stratalinker.  Printed arrays were stored dessicated at room temperature for less than 3 months prior to use.


title: 2007-05-17_C_elegans_ChIP_01

first: Everett

last: Zhou

description: Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

first: Susan

last: Strome

first: Jason

last: Lieb


title: Human Exon 1.0 ST Array [exon_ids based on HsEx10stv2_Hs_ENSE_probesetgroup.txt ]

status: Public on Dec 09 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

institute: Max Planck Institute for molecular genetics

description: Chip description file based on Ensembl v.46

first: Hugues

last: Richard

first: Marcel

middle: H

last: Schulz

first: Stefan

last: Haas

first: Asja

last: Nürnberger

first: Sabine

last: Schrinner

first: Daniela

last: Bazereit

first: Emilie

last: Dagand

first: Axel

last: Rasche

first: Hans

last: Lehrach

last: Vingron

first: Marie-Laure

last: Yaspo

manufacture_protocol: See manufacturer's web site


title: 2007-05-17_C_elegans_ChIP_03


title: Small RNAs from 4-week old seedling of Oryza sativa

status: Public on Dec 08 2008

city: Saint Louis

first: Xuefeng

state: MO

address: One Brooking Dr.

department: Department of Computer Science and Engineering

institute: Washington University in St. Louis

organism: Oryza sativa

description: Small RNAs were sequenced with 454 high-throughput pyro-sequencing platform at 454 Life Sciences


title: LC sciences Mouse microRNA v10

city: blacksburg

first: rujuan

last: dai

state: VA

address: 1410 price fork RD

department: CMMID

institute: virginia Tech

description: MicroRNA array platform

first: xiaochuan

last: zhou

manufacture_protocol: Array Protocol: LC Mir-Array-Prtl-060518. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Galbraith Laboratory Operon Arabidopsis thaliana 31.2K Long Oligonucleotide Microarray version 3.0 (ATv307.04.Z)

status: Public on Dec 03 2008

city: Tucson

first: David

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

organism: Arabidopsis thaliana

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv3.07.04.001-ATv3.07.04.300 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Laboratory, University of Arizona

middle: W


title: Zebrafish Paired End DiTags

city: Singapore

first: Chia

middle: Lin

last: Wei

address: 60 Biopolis Street, #02-01, Genome

institute: Genome Institute Of Singapore

organism: Danio rerio

description:
Paired End DiTags (PET) derived from 5 Zebrafish libraries.
Used a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization.
Mappings based on Genome Build: Zv6 (March 2006)

manufacture_protocol:
See full protocol in:
Gene Identification Signature (GIS) analysis for transcriptome analysis and genome annotation. Nature Method 2005 2(2):105-111.


title: Agilent-019119 Mouse miRNA Microarray 1.0 G4472A

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Agilent Mouse miRNA Microarray 8x15K (G4472A) annotated against the Sanger miRBASE 12.0 database of miRNAs. The microarray is designed to contain probes specific for each of the mouse miRNAs in Sanger miRBASE 10.1, as well as probes specific to the mouse viral miRNAs in this database.

Arrays of this design have barcodes that begin with 16019119 or 2519119.

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: UNL/Fromm-Arabidopsis thaliana-Illumina 1G Solexa ChIP-seq-Histone methylation H3K4

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Illumina 1G Solexa, Illumina Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA.


title: IHM Listeria monocytogenes whole genome 12k array

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

institute: Lehrstuhl für Mikrobiologie

description: Oligonucleotide sequence information may be found in GPL7062_sequence_oligos.txt linked below as a supplementary file.

manufacturer: Institute for Hygiene and Microbiology, University of Wuerzburg

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: AbC ELTE_human_960_v1

city: Budapest

first: József

last: Prechl

address: Pázmány Péter s. 1/C

department: Immunology Research Group

country: Hungary

institute: ELTE-MTA

description: Spotted antigens (protein, peptide, DNA … )

manufacturer: Eotvos Lorand University, Budapest, Hungary

manufacture_protocol:
Antigens were spotted in triplicates of three dilutions (1x, 5x, 125x) onto home made nitrocellulose chip. Dilutions were carry out in 0.05% Tween 20 containing PBS. BioOdyssey Calligrapher (Bio-Rad) was used for the printing with the following program:
sourceselect Run = No
substrate Type = Slides
Number of Slides in Y= 4
Number of Slides in X= 4
Slide Size = standard
Substrate Size in Millimeters in X= 75.500
Substrate Size in Millimeters in Y= 25.350
[Grid Layout]
Source plate Type= 384
Number of Source plate Rows= 8
Number of Source plate columns= 12
Number of Dips per Source plate= 96
Pin Type= solid
Pin Distance = 4.5mm
Number of pins in Y= 2
Number of pins in X= 2
Number of samples = 256
Number of Spots to be printed = 1536
Replicate Spots per Grid in X= 1
Replicate Spots per Grid in Y= 3
Use Advanced parameters = Yes
[Grid Advanced]
Top Left Grid Margin in x= 5.000 (mm)
Top Left Grid Margin in Y= 5.000 (mm)
Bottom Right Grid Margin in x= 8.150 (mm)
Bottom Right Grid Margin in Y= 5.000 (mm)
Distance between Spots in x= 550.000 (micron)
Distance between Spots in Y= 550.000 (micron)
No. of Spots per Grid in X= 8
No. of Spots per Grid in Y= 6
No. of Total Spots per Grid= 48
No. of Reprints of the Same Spot= 1
Grid printing Direction= Left-right, Top-down
No. of Different supergrids in x= 2
No. of Different supergrids in Y= 2
Total Number of supergrids= 4
Distance between supergrids in x= 4.500 (mm)
Distance between supergrids in Y= 4,500 (mm)
Supergrid printing Direcrion= Left-right, Top-down
No. of Duplicate supergrid clusters ln x= 2
No. of Duplicate supergrid clusters in Y= 1
Distance between Duplicate supergrid clusters in x= 17.675 (mm)
- Distance between Duplicate supergrid clusters in Y= 4.500 (mm)
No. of Full plates= 0
No. of Dips in the Last plate= 64
Total No. of Spots in a Grid= 48
Sample picking Direction= Top-down, Left-right
SubDips Exist= 0
SubDip Rows= 1
SubDip Columns= 1
Total SUbDips= 1
[Blotting]
Use blots= No
Blot slides Blot Distance= 450 (micron)
All Blotting slides are sufficient for= 11.666667 (plates)
[washing]
wash selection= Different samples
Pre-wash Step1= 2
Pre-wash Step1 Time= 2.500 (s)
Pre-wash step2= 1
Pre-wash Step2 Time= 2.000 (s)
Pre-wash Step3= 0
Pre-wash Step3 Time= 0.000 (s)
Main-wash cycles= 5
Main-wash Step1= 3
Main-wash Step1 Time= 3.000 (s)
Main-wash Step2= 1
Main-wash Step2 Time= 0.500 (s)
Main-wash step3= 0
Main-wash Step3 Time= 0.000 (s)
Post-wash Step1= 3
Post-wash Step1 Time= 3.000 (s)
Post-wash Step2= 2
post-wash Step2 Time= 5.000 (s)
Post-wash step3= 1
post-wash step3 Time= 0.500 (s)
[options]
Z-Down offset in sourceplate = 0.000 (mm)
Source plate Approach speed= 20.000 (mm/s)
Source plate Withdraw speed= 15.000 (mm/s)
Source plate Dwell Time = 1000.000 (ms)
oscillation in water-bath1 = Yes
oscillation in Water-bath2 = Yes
Water-bath1 Oscillation Distance in x= 4.000 (mm)
water-bath2 Oscillation Distance in x= 1.500 (mm)
water-bath1 Number of oscillations in Bath= 3
water-bath2 Number of oscillations in Bath= 3
Z-Down offset on slides = 0.000 (mm)
Slide/Membrane/Blot Approach speed= 10.000 (mm/s)
Dwell Time for printing= 25.000 (ms)
Number of substrates between Redips = 0
Number of Redips per sample = 1


title: SAGE:10:NlaIII:Rattus norvegicus

status: Public on Nov 13 2001

last: GEO

organism: Rattus norvegicus

technology: SAGE NlaIII


title: SAGE:17:NlaIII:Rattus norvegicus

status: Public on May 25 2007

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


title: ISQ Chip Folsomia candida Collembola VU 15.7K version 2.0

status: Public on Aug 09 2008

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

institute: Sanquin

organism: Folsomia candida

description: 8*15K format. In total 5,069 different experimental probes representing 5,069 EST contigs are in triplicate on the microarray. All probes were also on the previous version (1.0) of the Folsomia candida chip (GPL6381).

first: Nico

last: van Straalen

first: Dick

last: Roelofs

manufacture_protocol: 60-mer oligo probes were designed from Collembase EST contigs, using OligoArray v2.0 and synthesized in situ by an ink-jet printing (Agilent) method on glass slides.