title: Agilent-012097 Human 1A Microarray (V2) G4110B - alternative version

status: Public on Nov 08 2007

city: RTP

first: Min Ok

last: Song

state: NC

address: 111 T.W. Alexander Dr

department: DIR ETP

country: USA

institute: NIEHS

organism: Homo sapiens

technology: in situ oligonucleotide

description:
This is an alternative version of the official Agilent platform assigned accession number GPL887. The ID column includes the Agilent probe identifiers instead of the Agilent feature IDs.
Agilent's Human 1A Oligo Microarray (V2) includes over 20K 60-mer oligonucleotide probes, sourced from the Incyte Foundation Database, RefSeq, and GenBank, and are designed to span conserved exons across the transcripts of the targeted full length genes. Coupled with Agilent's probe selection and validation processes, this design method gives the customer maximum confidence in data quality and prevents redundancy in gene coverage.

distribution: commercial

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


title: Illumina Genome Analyzer (Schmidtea mediterranea)

status: Public on Sep 30 2009

last: GEO

organism: Schmidtea mediterranea

technology: high-throughput sequencing

distribution: virtual


title: 454 GS FLX (Schmidtea mediterranea)


title: Illumina Genome Analyzer (Sarcophilus harrisii)

organism: Sarcophilus harrisii


title: Illumina Genome Analyzer II (Drosophila erecta)

status: Public on Sep 29 2009

organism: Drosophila erecta


title: 454 GS FLX (Medicago truncatula)

organism: Medicago truncatula


title: Illumina Genome Analyzer (Locusta migratoria)

status: Public on Sep 28 2009

organism: Locusta migratoria


title: LC_MRA-1001_miRHuman_10.1_071219 [condensed version]

city: Dallas

first: Zain

last: Paroo

state: TX

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern Medical Center

description:
This array represents a condensed version of GPL8363.
Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1

distribution: custom-commercial

first: Christoph

last: Eicken

manufacture_protocol: 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, http://microrna.sanger.ac.uk/sequences/) 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: Illumina Genome Analyzer II (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: Illumina Genome Analyzer (Monosiga brevicollis)

organism: Monosiga brevicollis


title: Bacillus cereus Bc14579 - 1st design

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

country: Netherlands

institute: Wageningen University

organism: Bacillus cereus ATCC 14579

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

first: Douwe

last: Molenaar

first: Menno

last: van der Voort

first: Willem

last: van Schaik

manufacture_protocol:
Agilent manufacture protocol.
Agilent uses its inkjet technology to print oligos onto glass slides.


title: Illumina Genome Analyzer II (Brachypodium distachyon)

organism: Brachypodium distachyon


title: MGAC_Ecoli_v1.0

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

organism: Escherichia coli

technology: spotted oligonucleotide

first: Jihyun

middle: F

last: Kim

first: Sung-Ho

first: Haeyoung

last: Jeong

first: Dong-Su

last: Yu

manufacture_protocol: Oligonucleotide microarrays were fabricated by which both E. coli B REL606 and K-12 MG1655 could be tested for the synthesis of both common and unique mRNAs. Probes (70-mers) were designed by Array Designer (Premier Biosoft International) and cross-hybridization was checked by BLASTN. A total of 4,819 probes were synthesized by Illumina. The probes represented 3,762 genes that shared over 80-mer of sequence in the two E. coli strains, 382 genes found uniquely in REL606, and 534 genes unique to MG1655. The other probes were positive and negative controls. The probes were spotted in duplicate onto a GAPSII glass slide (Corning Inc.) by Digital Genomics in Seoul, Korea.


title: Illumina Genome Analyzer (Bos taurus)

organism: Bos taurus


title: Illumina Genome Analyzer (Nematostella vectensis)

organism: Nematostella vectensis


title: Illumina Genome Analyzer (Branchiostoma belcheri)

organism: Branchiostoma belcheri


title: Illumina Genome Analyzer II (Triticum aestivum)

organism: Triticum aestivum


title: University of Chicago - tRNA Custom Array - 8736 - v1.0

city: Chicago

first: Tao

last: Pan

state: IL

address: 929 East 57th street

department: Biochemistry & Molecular Biology

institute: University of Chicago

organism:
Saccharomyces cerevisiae
Homo sapiens
Caulobacter vibrioides

manufacture_protocol: See manufacturer website.


title: Illumina Genome Analyzer (Amphimedon queenslandica)

organism: Amphimedon queenslandica


title: Illumina Genome Analyzer (Medicago truncatula)


title: Illumina Genome Analyzer II (Oryza sativa)

organism: Oryza sativa


title: AB SOLiD System 3.0 (Mus musculus)

organism: Mus musculus


title: Illumina Genome Analyzer (Trichoplax adhaerens)

organism: Trichoplax adhaerens


title: Harvard_Human_BeadChip_23K_Ref8v3

city: Boston

first: Je

middle: Hyuk

last: Lee

state: MA

address: 3 Blackfan Circle, CLSB 528

department: Wyss Institute

institute: Harvard Medical School

organism: Homo sapiens

technology: oligonucleotide beads

first: Jehyuk

first: In-Hyun

last: Park

first: Nimet

last: Maherali

first: Jie

last: Deng

first: Jun

last: Li

first: Jin

middle: B

first: Konrad

last: Hochedlinger

first: George

middle: Q

last: Daley

first: Kun

last: Zhang

middle: M

last: Church

manufacture_protocol: See manufacturer's website


title: Roche AmpliChip Leukemia Custom Microarray

city: Pleasanton

first: Wei-Min

last: Liu

state: CA

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

manufacture_protocol: see manufacturer's web site


title: Agilent Mouse array 105k

city: Houston

first: Richard

last: Kellermayer

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
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.
This platform is based on NCBI build 36.

manufacture_protocol: Agilent Technologies


title: Cryptococcus neoformans H99 gene expression microarray version 1

city: Baltimore

first: Clara

last: Bien

state: MD

address: 725 N. Wolfe St Physiology rm #107

department: Cell Biology

institute: Johns Hopkins University

organism: Cryptococcus neoformans

description: Agilent custom expression array design #020071

manufacture_protocol:
1. Arrays were designed using Agilent eArray software
2. Custom gene expression arrays were generated by Agilent Technologies in their 8X15K format


title: 2005-09-13_Dros_300bp_60mer

status: Public on Sep 25 2009

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

organism: Drosophila melanogaster

description:
Release 4 genome from the Berkeley Drosophila Genome Project (BDGP).
60-bp probes at approximately 300 bp intervals, preferably no GATC sequences, CG content as close to 50% as possible, non-repetitive.

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


title: Mouse cDNA NIA - Australian library

status: Public on Sep 26 2009

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

country: Australia

institute: SA Pathology

technology: spotted DNA/cDNA

description: A cDNA array manufactured around 2002, 2003 in Australia.  This version contains duplicate spots.

distribution: non-commercial

manufacturer: Australian Genome Research Facility Ltd (AGRF)

manufacture_protocol: Please request from AGRF


title: NimbleGen Canis familiaris 385K CanFam2_WG_CGH

city: Vancouver

first: Bradley

middle: P

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

organism: Canis lupus familiaris

description: Dog 2.0

manufacture_protocol: see the manufacturer's website


title: JCVI PFGRC Streptococcus mutans 13K v3 array designed primarily based on strain UA159

status: Public on Sep 24 2009

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus mutans

description: This set includes 1948 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 3QSM, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Illumina Genome Analyzer (Ciona intestinalis)

last: GEO

organism: Ciona intestinalis


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain MW2

organism: Staphylococcus aureus

description: This set includes 4510 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 8QSA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Vibrio cholerae 13K v3 array designed primarily based on strain N16961

organism: Vibrio cholerae

description: This set includes 3754 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 3QVC, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: 454 GS FLX (synthetic construct)

status: Public on Sep 23 2009

organism: synthetic construct


title: DKFZ SC112 / human 9k BAC chip (3k V6 - r24)

status: Public on Sep 22 2009

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
Spotted genomic DNA fragments from bacterial artificial chromosomes (BACs).
Keywords = spotted
Keywords = human

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

first: Bernhard

last: Radelwimmer

first: Peter

last: Lichter

manufacture_protocol: DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system,BioRad, Munich, Germany) at 20C and 40% humidity. After spotting, slides were cross-linked,baked for 1 hr at 80C, and cross-linked again.


title: DKFZ SC137 / Operon Human 38k V4.0 + 10q22p - r6

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

first: Sebastian

last: Barbus

first: Meinhard

last: Hahn

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: Print_906

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

organism: Helicobacter pylori

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: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain CG8421

organism: Campylobacter jejuni

description: This set includes 6982 oligonucleotides, has 23232 spots distributed in 48 blocks.

manufacture_protocol: 2QCJ, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Trypanosoma brucei Strain 927 Oligonucleotide Tiling Array

first: Dhileep

last: Sivam

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

organism: Trypanosoma brucei brucei TREU927

description:
60mer probes were designed to known coding regions of Trypanosoma brucei strain 927,  Approximately 8 probes per gene were designed to each of the 8562 protein coding genes, and 3 probes were designed to each RNA gene.  Each probe was placed on the chip in triplicate.  Remaining space on the array was fillied with 50mer probes spaced evenly through unnannotated regions of the genome, though these probes were not considered in the final analysis.  Only one copy of each unnannotated region probe was placed on each chip.

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

Native NimbleGen files (ndf, ngd) are also linked as supplementary files.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Colorado State University Mycobacterium tuberculosis V20071007

first: Petros

last: Karakousis

address: 1550 Orleans street

department: Medicine

institute: John Hopkins University school of medicine

organism: Mycobacterium tuberculosis H37Rv

description: The Tuberculosis Genome Oligo Set consists of 70mer probes representing 4,269 M. tuberculosis (H37Rv and CDC1551) genes, plus 26 controls. The probes were designed from the predicted genomic sequence of the best-characterized M. tuberculosis strain, H37Rv, obtained from the Sanger Center (Cambridge, UK) and The Institute for Genomic Research (Rockville, MD, USA). An additional 371 probes were designed from the CDC1551 strain. The probes are Tm normalized to 79°C.

manufacturer: Colorado State University TB Vaccine Testing and Research NIH, NIAID Contract No. HHSN266200400091C

first: Dalin

last: Rifat

manufacture_protocol: Oligonucleotide 70mers were generated from whole genome sequence within coding regions. Features were designed to have similar hybridization temperatures. Samples were spotted and pre-processed using standard procedures from the lab of Rocky Mountain Regional Center of Excellence.


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain N315


title: Institute for Systems Biology NimbleGen Halobacterium 391k tiling array

first: Tie

last: Koide

address: 1441 N 34th street

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

first: Koide

last: Tie

first: Facciotti

last: Marc T.

first: Reiss

last: David J.

first: Baliga

last: Nitin S.

manufacture_protocol: see http://www.nimblegen.com/technology/manufacture.html for details


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain Mu50


title: Illumina Genome Analyzer (Solanum lycopersicum)

status: Public on Sep 21 2009

organism: Solanum lycopersicum


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain USA300


title: Illumina Genome Analyzer (Arabidopsis lyrata)

status: Public on Sep 11 2009

organism: Arabidopsis lyrata


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain MSSA476


title: Bovine Long Oligo Plus Array (BLOPlus) 10K

status: Public on Sep 15 2009

city: Guelph

first: Chris

last: Verschoor

state: ON

address: 50 Stone rd. East

department: APS

institute: University of Guelph

organism: Bos taurus

manufacturer: Michigan State University, Center for Animal Functional Genomics

manufacture_protocol:
Original BLO:
The CAFG’s mission to improve specificity, slide reproducibility, spot
morphology, background and ease-ofuse led to the work in 2004 on a bovine long oligo (BLO) microarray. This set of 70-mer oligos was derived from 13,914 ESTs in the NBFGC library. Using the Basic Local Alignment Search Tool (BLAST), sequences from NBFGC were compared to the Reference Sequence (RefSeq-2004) database at the National Center for Biotechnology Information (NCBI). This search yielded 7,449 unique
genes. Oligo design was performed by bioinformaticians at the CAFG and the oligos were manufactured by Operon Biotechnologies, Inc. BLO slides were first printed in early 2005.
BLO + extension set = BLOPlus:
The BLOPlus microarray is a second generation bovine long oligo set.
BLOPlus contains all oligos from the original BLO microarray plus an
additional 1,865 bovine sequences. These sequences were selected from the highly published BOTL cDNA microarray library. BOTL originated from a
normalized EST library derived from bovine leukocytes. The original
microarray contained 720 unique, sequenced genes. Over the years other
genes were added to the BOTL microarray, including a set of PCRgenerated sequences, eventually totaling 1,391.
The aging BOTL cDNA resource needed to be updated and replaced.
Producing an extension set of 70-mer oligos filled this need. The extension set also added genes important for studying bovine immunobiology to our bovine oligo microarray. A search in The Institute
for Genomic Research (TIGR) database for the 1,391 BOTL sequences
yielded a match to 1,330 of these sequences. Fifteen Kyoto  encyclopedia of Genes and Genomes (KEGG) pathways were also investigated yielding another 550 sequences. Many of the genes selected had TIGR tentative consensus (TC) 70-mer sequences. These were used for the oligos where available. A total of 305 70-mer sequences were generated by the CAFG using OligoPicker1 software.
New oligo sequences were manufactured by Operon Biotechnologies, Inc.
in January 2008. The sequences for all of the 70-mer oligos that appear on BLOPlus (Box taurus (bovine) AROS V1.1) are available for download at www.operon.com in the Oligo Microarray Database (OMAD).
The BLOPlus microarray is printed at the Research Technology Support
Facility (www.rtsf.msu) at Michigan State University. The substrate is the SuperAmine slide from ArrayIt Microarray Technologies
(www.arrayit.com). This substrate contains positively charged, linear
primary amines attached covalently to the glass surface allowing for
attachment of the negatively charged DNA backbone.


title: IQUSP Human Intron-Exon 44k v2.0

status: Public on Sep 18 2009

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

country: Brazil

institute: Universidade de Sao Paulo

organism: Homo sapiens

first: Helder

middle: I

last: Nakaya

first: Paulo

last: Amaral

first: Rodrigo

last: Louro

first: Sergio

last: Verjovski-Almeida

first: Eduardo

last: Reis

manufacture_protocol: Agilent’s non-contact industrial inkjet printing process uniformly deposits oligo monomers onto specially-prepared glass slides. Custom microarrays are manufactured using Agilent’s non-contact in situ synthesis process of printing 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. This is achieved with an inkjet process which delivers extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. Precise quantities are reproducibly deposited “on the fly.” This engineering feat is achieved without stopping to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability.


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain MRSA252

first: PFGRC

last: JCVI


title: Nimblegen Hg18 tiling array for AIRE regulated genes

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

first: Ana

last: Rebane

first: Kai

last: Kisand

first: Martti

last: Laan

first: Uku

last: Haljasorg

first: Reidar

last: Andreson

first: Pärt

last: Peterson

manufacture_protocol: Roche NimbleGen's proprietary, light-mediated synthesis producing high-density microarrays of long oligonucleotide probes (50-75mer).


title: JCVI PFGRC Staphylococcus aureus 16K v8 array designed primarily based on strain COL


title: Arabidopsis thaliana microRNA 0.35K microarray

city: Bethesda

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

organism: Arabidopsis thaliana

first: Zengjian

middle: J

last: Chen

first: Vanitharani

last: Ramachandran

first: Xuemei

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer (Citrus sinensis)

last: GEO

organism: Citrus sinensis


title: Illumina Genome Analyzer II (Trypanosoma brucei gambiense)

organism: Trypanosoma brucei gambiense


title: Mus musculus 22K Mm22k_oligo_v2Bpl_10m111104

city: Singapore

first: Martin

middle: Lloyd

last: Hibberd

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

country: Singapore

institute: Genome Institute of Singapore

organism: Mus musculus

manufacturer: Genome Institute of Singapore Microarray Facility

manufacture_protocol: 60 mer oligonucleotide probes were spotted onto poly-L-lysine-coated microscope slides using GeneMachines OmniGrid Microarray Spotter (USA).


title: Homo sapiens 41.7K Print_926

status: Public on Sep 08 2009

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University


title: Homo sapiens 41.7K Print_931


title: NimbleGen_Rhesus macaque_38K_DNA methylation array

status: Public on Sep 10 2009

city: Rehovot

first: Amos

last: Tanay

address: The Weizmann Insititute

department: Computer Science and Applied Math

country: Israel

institute: The Weizmann Institute

organism: Macaca mulatta

description:
Annotation in this record based on the NCBI Jan. 2006 rhesus macaque (Macaca mulatta) draft assembly — v.1.0.

Array Design: We collected a set of human ESC bivalent domains (Bernstein, Mikkelsen et al. 2006), and combined them with additional methylation related domains and control regions. We mapped these regions from the human genome to the rhesus genome using the UCSC liftOver program and tiled them with probes at 100 bp resolution (Roche-Nimblegen).

080318_Tanay_RockefellerU_RheMac2_ChIP.ndf and 080318_Tanay_RockefellerU_RheMac2_ChIP.pos included as supplementary files

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


title: Max Planck Institute, Whole Genome Array for Rhodopirellula baltica SH1T 7.4K version 1

status: Public on Sep 09 2009

city: Bremen

first: Patricia

last: Wecker

address: Celsiusstr, 1

department: Molecular Ecology

institute: Max Planck Institut for Marine Microbiology

organism: Rhodopirellula baltica SH 1

description:
Strain: Rhodopirellula baltica SH 1T
spotted Whole Genome Array available by Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany

first: Andreas

last: Ellrott

first: Chrstine

last: Klockow

first: Frank

middle: O

last: Glöckner

first: Chris

middle: A

last: Würdemann

manufacture_protocol:
70mer oligos designed and synthesized by operon (www.operon.com)
Pirellula Aros 1.0


title: Homo sapiens 43.1K Print_849


title: Caenorhabditis remanei small RNAs (454 GS FLX system)

status: Public on Sep 07 2009

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

institute: University Medical Center Groningen

organism: Caenorhabditis remanei

technology: other

manufacturer: Hubrecht Institute-KNAW & Univeristy Medical Center Utrecht

first: E

last: de Wit

first: S

last: Linsen

last: Cuppen

manufacture_protocol: small RNA deep sequencing


title: Aalborg University Illumina human-6 v2.0 expression beadchip

city: Aalborg

first: Vladimir

last: Zachar

address: Fredrik Bajers Vej 3B

country: Denmark

institute: Aalborg University

description: The official commercial Illumina human-6 v2.0 expression beadchip is assigned accession number GPL6102. This platform was created to align with Bioconductor normalized data output.

manufacture_protocol: Illumina Beads; see manufacturer's website


title: Utz Lab Whole Protein Autoantigen Array V1.0

first: Chih Long

last: Liu

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

organism:
Escherichia coli
Gallus gallus
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Mus musculus

technology: spotted peptide or protein

first: Imelda

last: Balboni

first: Cindy

last: Limb

first: ChihLong

first: Michael

last: Kattah

first: Paul

last: Utz

manufacture_protocol: Whole protein or synthetic peptide antigens were purchased from commercial vendors as described in the data table.  Antigens were resuspended in 0.2 mg/ml in 1X phosphate-buffered saline (PBS) pH 7.4.  Custom microarrays were printed with the Bio-Rad Chip Writer Pro on Whatman FAST slides, with each antigen printed in 6 replicates.  Arrays were stored vacuum-packed for up to 2 months at 4 degrees Celsius before use.


title: Stanhope_S. uberis_2k_design1_#4231

status: Public on Sep 13 2009

city: Ithaca

last: Stanhope

state: NY

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

organism: Streptococcus uberis

description: This array represents a condensed verion of full array, which is linked as a supplementary file below.


title: Homo sapiens 41.5K Print_1009

first: Jonathan

last: Pollack


title: Caenorhabditis briggsae small RNAs (454 GS FLX system)

organism: Caenorhabditis briggsae


title: Kyushu University Clostridium perfringens strain 13 DNA 27K microarray version 1

status: Public on Sep 17 2009

city: Fukuoka

first: Hideki

last: Hirakawa

state: Fukuoka

address: 6-10-1, Hakozaki, Higashi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

organism: Clostridium perfringens str. 13

manufacturer: Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

manufacture_protocol:
2723 genes and 144 intergenic regions of strain 13 were amplified by PCR with gene-specific primers and PCR products were confirmed by gel electrophoresis
In total, 2867 probes were spotted onto poly-L-Lysine coated glass slides in twice (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).


title: Synovial protein array 0.5K v1.0

status: Public on Sep 12 2009

first: William

last: Robinson

address: 269 Campus Dr

organism:
Homo sapiens
Mus musculus

manufacturer: Robinson Lab, Stanford University School of Medicine

first: Peggy

last: Ho

first: Lowen

middle: Y

last: Lee

first: Xiaoyan

last: Zhao

first: Beren

middle: H

last: Tomooka

first: Ricardo

middle: T

last: Paniagua

first: Orr

last: Sharpe

first: Maya

last: BenBarak

first: Wolfgang

last: Hueber

first: Piyanka

middle: E

last: Chandra

first: Lawrence

last: Steinman

manufacture_protocol:
Microarray Printing Protocol
1. Load Arraymaker software, select Connect tab, and click on Connect to Controller button.
2. Select Home all axes.
3. Place test pins in print head and use the arrow buttons in the Align tab to align the print head with respect to the sonicator, vacuum block, print plate, and print platter.
4. Click set to save settings.
5. Replace test pins with 16 pins intended for use during the print and select Test Print tab.
6. To verify that pins are sliding up and down without sticking and delivering liquid at every spot, perform a test print using 1X PBS. If the test print is not satisfactory, replace malfunctioning pins or try doing a series of wash/dry cycles.
7. When ready to print, select Print Run tab and place slides on the print platter, securing them with tape.
8. Thaw and vortex first print plate (384-well plates containing antigens at a concentration of about 0.2 mg/ml). Centrifuge print plate at 2000 rpm for about 5 seconds. Place and secure the print plate on print platter.
9. Set the Print Setup to the following values (Number of plates = 6, Tips = 16, Spots per load = 1, Entire Platter = check, Re-fill = check, Slow Pick Up = uncheck).
10. Set Station Settings to the following values (Wash Cycles = 4, Wash time = 4000, Dry time = 3000, Load Time = 1000, Bounce Dry = uncheck, Swish Wash = check).
11. Leave the Start Settings as is and make sure Tandem Print = uncheck.
12. Set the Slide Setup to the following values (Begin on Slide 1, End on Slide 137, Sector Width = 12, Spacing = 340).
13. Leave the Blot Pad Settings as is and make sure Use Blot Pad = Uncheck.
14. Click Start button.
15. The machine runs for ~ 8 hours (The print uses duplicates of three unique print plates for a total of six print cycles). Re-seal each used print plate with plate foil after each print.
16. After all three print plates have been printed, sonicate pins for 10 minutes and then dry for 10 seconds thoroughly to clean the tips.
17. Remove all the tape and slides from the platter.
18. Put the slides back into a slide box and store at 4ºC until ready to probe.
GAL File Generation Protocol
1. In Excel, enter the appropriate header information including Axon Text File version, number of header lines and data columns, file type, and block information.
2. Fill out the data columns (Block, Column, Row, Names).
3. Save the file in Excel (*.xls) format as: print_YYYY_MM_DD_array_list_for_gal.xls, where YYYY is the year, MM is the month, and DD is the day the slides were printed.
4. Save the file in text (Tab delimited) (*.txt) format
For example: print_YY_MM_DD_array_list_for_gal.txt
5. Select File, Close (or Exit). Excel will ask about saving changes. Click No and Excel will end.
6. Launch Notepad and open the GAL file in the *.txt format.
7. Change all the triple quotes (“””) to single quotes (“).
8. Save and exit Notepad
9. Launch Windows Explorer and change the folder options to show the file extensions
10. Select Tools, Folder Options…,
11. Select the View Tab
12. Uncheck the box Hide file extensions for known file types
13. Select OK
14. Find the GAL file in the *.txt format
15. Create a copy of the print_YY_MM_DD_array_list_for_gal.txt
16. Right click on the print_YY_MM_DD_array_list_for_gal.txt file and rename it as: print_YY_MM_DD_array_list_for_gal.gal


title: UCLA-MEMLAB HP 1543 Version 2

status: Public on Sep 14 2009

city: Los Angeles

first: Yi

last: Wen

address: 11301 Wilshire Blvd., Bldg.113, Rm. 324

department: Physiology Department

institute: UCLA/VAGLAHS

organism: Helicobacter pylori

manufacturer: TeleCom International, Inc. ArrayIt Division

first: George

last: Sachs

manufacture_protocol:
1. PCR products that contained 1,534 predicted open reading frames (ORFs) of Helicobacter pylori strain 26695 were purchased from ResGen-Invitrogen Corporation.
2. The concentration of PCR product was estimated based on the density of the band on ethidium bromide-stained agarose gel.
3. After purification of the PCR products using QIAquick 96-well PCR purification kit (Qiagen), ~4 µg of PCR product for each ORF was loaded into a fresh 384-well Flex Chips Source plate provided by TeleChem International, Inc.
4. After completely dry the plates with Speed-Vacuum, the dried DNA plates were re-suspended by adding 5 µl of Micro Spotting Plus (ArrayIt, Cat.# MSP) to each well for printing (TeleCom Internalional, Inc. ArrayIt).


title: Oryzon Human Exon SI Array

status: Public on Sep 05 2009

city: PAMPLONA

first: David

last: Blanco

address: Avda Pio XII, 55

department: Area Oncology

country: Spain

institute: CIMA

first: Elena

last: Aibar

first: Alvaro

last: Perdones

manufacture_protocol: See manufacturer's website


title: Stanhope_S. uberis_2k_design2_#4887

first: Michael

last: Stanhope


title: Synovial protein array 0.5K v2.0

first: William

last: Robinson


title: Agilent 15K Wheat seed specific microarray

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

organism: Triticum aestivum

description: Oligos were annotated to several databases (http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=wheat) (http://plantta.jcvi.org/cgi-bin/plantta_release.pl) (http://www.genome.jp/kegg/pathway.html) where the there is at least 97% of homology between the sequence of oligo and correspondig contig/gene.

last: Fehér

manufacture_protocol: The manufacture protocol can be found on the web page of Agilent company (http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/pages/gp38516.aspx)


title: Agilent-015060 Magnaporthe grisea 2.0 4 X 44K (Probe name version)

status: Public on Sep 16 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Pyricularia grisea

description:
This Magnaporthe grisea 2.0 microarray contains oligos designed after 15,170 predicted Magnaporthe genes and transcripts from the newly annotated data set at the Fungal Genomics Laboratory at North Carolina State University.

The ID column represents the Agilent probe names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL9201.

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


title: Illumina Genome Analyzer (Chlamydomonas reinhardtii)

status: Public on Sep 04 2009

last: GEO

organism: Chlamydomonas reinhardtii


title: Illumina Genome Analyzer (Naumovia castellii)

status: Public on Sep 02 2009

organism: Naumovozyma castellii


title: Kyoto University Custom Agilent Ciona intestinails 242K Tiling Array No.2 (of 2)

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

organism: Ciona intestinalis

first: Yutaka

last: Satou

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: Homo sapiens 41.6K Print_933

first: Jonathan

last: Pollack

organism: Homo sapiens

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


title: Illumina Genome Analyzer (Vanderwaltozyma polyspora)

organism: Vanderwaltozyma polyspora


title: Pristionchus pacificus small RNAs (454 GS FLX system)

first: Eugene

last: Berezikov

organism: Pristionchus pacificus

first: E

last: de Wit

first: S

last: Linsen

last: Cuppen


title: Homo sapiens 44.5K Print_1365


title: Caenorhabditis elegans small RNAs (454 GS FLX system)

organism: Caenorhabditis elegans


title: UON_Campylobacter oligo array v1

status: Public on Sep 01 2009

city: Leicestershire

first: Amy

last: John

address: Loughborough

institute: University of Nottingham

organism:
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Campylobacter jejuni RM1221
Campylobacter coli RM2228

first: Andrew

last: Scott

last: Timms

first: Ayman

last: El-Shibny

first: Philippa

last: Connerton

first: Ian

manufacture_protocol: The slides prepared for microarray were γ APS coated, A+ bar-coded Schott nexterion slides. The slides were printed according to Campylobacter dense array gal by Microgrid II GOD robot using TAS software version V2.4.03. This had 2500 pins with a 26 x 26 pin grid configuration. The spacing between the spots was 0.165 mm and the slides were rehydrated by incubation at room temperature in a humidity chamber for 30 min followed by a 30 min incubation at 60 ºC to dry. The slides were blocked in a solution containing 100 mM ethanolamine, 1 M Tris (pH 9.0), and 0.1% SDS for 15 min at 50 ºC, then thoroughly rinsed with water and spun dry. The slides contain duplicate sets of oligonucleotides representing the genomes of C. jejuni NCTC11168, RM1221 and C. coli RM2228. The arrays are based on the genomes of C. jejuni 11168, C. jejuni RM1221, C. coli RM2228 along with any miscellaneous genes and plasmids from other strains available in the database. They are composed of synthetic oligonucleotide 70-mers: Tm 71 °C ± 5 °C, location from 3’ end of gene >70 bp, poly (N) tract <8 bp, stem length in potential hairpin <8 bp contiguous bases common to any non-self ORF <20 bp, cross-hyb identity to all other genes <70%.


title: Illumina Genome Analyzer (Oryza sativa)

status: Public on Sep 03 2009

organism: Oryza sativa


title: Illumina Genome Analyzer (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Arabidopsis thaliana 34K NARC serie 1

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

organism: Arabidopsis thaliana

description: Norwegian Arabidopsis Research Center (NARC)

manufacturer: Norwegian Microarray Consortium, Trondheim

first: Atle

last: Bones

first: Torfinn

last: Sparstad

first: Hallgeir

last: Bergum

manufacture_protocol:
1. Oligos used in the production of the microarrays are from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0, while the custom made oligos were produced by Operon (Alameda, CA, USA) or MWG (Ebersberg, Germany). Information about the AROS probes is available at: http://omad.operon.com/arabidopsis/
2. Oligos are arrayed in Genetix X6004 384 well plates with V-shaped bottom. Each well contain 600 pmol 70 mer oligo
3. Oligos were resuspended in 16 µl Milli-Q-filtered DNase free water and 8 µl from each well were transfered to new set of Genetix X6004 384 well plates using a Tecan Genesis RSP 200 liquid handling workstation.
4. 8 µl DMSO were added to each well giving a final oligo consentration of ~20 µM and 50% DMSO.
5. The plates were sealed with ABgene Adhesive PCR Foil seals and centrifuged at 1000 rpm in a Sorvall RT6000B centrifuge. The plates were stored at -20C.
6. The plates were thawed and placed on a rotary shaker for 12 hour before printing of oligos.
7. The oligos were printed on amino silane coated UltraGaps slides (Corning, NY, USA) using a BioRobotics MicroGrid II robot (Genomic Solutions, MI, USA).
8. After printing the micorarray slides were exposed for UV light in a Stratalinker 2400 UV crosslinker (Stratagene), at 800 milijoules/cm2.
9. Microarray slides were stored under low humidity conditions and not exposed to light.


title: Illumina Genome Analyzer (Zea mays)

last: GEO

organism: Zea mays


title: NIAS Designed Custom Agilent Bovine 11K Oligo Microarray Ver2

status: Public on Sep 06 2009

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

institute: National Institute of Agrobiological Sciences

organism: Bos taurus

first: Toru

last: Takahashi

first: Misa

last: Hosoe

first: Kanako

last: Kaneyama

first: Ken-Go

last: Hayashi

first: Keiichiro

last: Kizaki

first: Kazuyoshi

last: Hashizume


title: Agilent Burkholderia cenocepacia 017397 microarray

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

organism: Burkholderia cenocepacia

manufacture_protocol: Agilent


title: 454 GS (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Illumina Genome Analyzer II (Bombyx mori)

organism: Bombyx mori


title: Affymetrix GeneChip Rat Genome 230 2.0 Array [CDF: Brainarray Version 11, Rn230_Rn_ENTREZG]

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

organism: Rattus norvegicus

relation: Alternative to: GPL1355 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Arabidopsis Tiling 1.0R [TAIR7-based custom CDF, ORF version]

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

description:
Affymetrix Whole Genome Tiling Array Chip designed by the Salk Institute and Affymetrix.

Chip Definition File based on TAIR7 genome as reported in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94 (PMID: 18764924).  The CDF file for use in R is included as a supplementary file.


title: UNM Biomphalaria glabrata 70-mer oligo array version 1

city: Albuquerque

first: Coen

last: Adema

state: NM

address: 1 University of New Mexico

department: CETI Biology MSC03 2020

country: USA

institute: University of New Mexico

organism: Biomphalaria glabrata

first: Eric

middle: S

last: Loker

manufacture_protocol: The 1,152 oligonucleotides (70-mers) supplied by IDT, originally provided at a 6nM concentration, were resuspended in deionized water to a concentration of 100μM. They were further diluted into 50% water and 50% ESB (Epoxide Spotting Buffer, Integrated DNA Technologies, Coralville, IA) to a final concentration of 40μM for spotting on the microarray. Twenty microliters of each oligonucleotide was transferred to 384 well microarray plates (Genetix, Queensway, New Milton, Hampshire, UK). A total of 300 Epoxide-coated glass slides (Corning Life Sciences, Lowell, MA) were spotted using the QArray Max (Genetix, Queensway, New Milton, Hampshire, UK) and dried for one hour at 80% humidity and then overnight at 60% humidity. A 24 pin microarraying head was used to print the slides. The plate type selected was for a 10μl calibration even though there was 20μl of sample per slide. Eight landing lights (consisting of 5μM Cy5 labeled oligo, 5μM Cy3 labeled oligo, 40μM of unlabeled oligo (GCF3), and ESB) were printed on every subarray for orientation. The printing conditions consisted of 630 stamps/ink and 1 stamp/spot. The stamp time for each spot was 20ms (milliseconds) and the total inking time was 9999ms. A total of 2 touch-offs per inking were used and lasted 4000ms. The sterilization cycle used included 10000ms wash time and 35000ms dry time. All samples were printed first and the markers printed last.Three replicates of each oligo were printed in each field, resulting in 6 replicate spots per slide. Replicates were spotted so that they were not adjacent to each other. A total of 48 subarrays with dimensions 12 x 13 spots were printed on each slide resulting in a 7,488 feature array. All slides were stored in a dessicated mircro array cabinet until use.


title: Homo_sapiens_array_hg18_NimbleGen

city: Cambridge

first: Christian

last: Metallo

address: 77 Mass. Ave.

department: Chemical Engineering

institute: Massachusetts Institute of Technology

manufacture_protocol: refer to Nimblegen


title: Illumina Genome Analyzer (Saccharomyces bayanus)

organism: Saccharomyces bayanus


title: CCHMC_Nimblegen_zebrafish_32K_Zv6

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

organism: Danio rerio

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol:
Organism: Danio rerio
Source: Ensembl and UCSC
Build: Zv6
Probe Length: 60mer
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number A6183-00-01
Design Name 2007-03-01 Zv6 60mer EXP
Description Danio rerio 1-Plex Array
Genes 32,292
Probes/ Target 12
Features 385,000
Replicates 1
from www.nimblegen.com
Array Synthesis
NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system. At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays. These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
Hybridization
NimbleGen Systems has developed a proprietary hybridization system, including protocols, buffers, hybridization cassettes, hardware, and temperature control instrumentation that generate highly reproducible and sensitive hybridizations. These protocols have been optimized to require minimum amounts of sample, while providing a hybridization volume that can be continually mixed over the time-course of the incubation. This method generates arrays with extremely high inter-array reproducibility (up to r2>0.99) and very low intra-array coefficient of variation (cv < 12%) across the array surface. In a typical gene expression experiment, each gene is represented by a minimum of 10 and as many as 25 probe-pairs complementary to different portions of the mRNA transcript. This guarantees that at least 10 independent measurements of mRNA concentration are included in the final value for the expression level for the gene, resulting in more reliable and reproducible gene expression calculations. In addition, these 10 to 25 probe-pairs are distributed evenly across the surface of the array. This distribution effectively eliminates problems associated with any local variation in the spatial uniformity or noise in the hybridization, because expression values are derived from a minimum of ten different locations on the array.


title: Genotoul/Biopuces Eurogentec Yeast 6K 20x21

city: Toulouse

first: Laurent

last: Benbadis

address: 135 Av de Rangueil

institute: LISBP INSA CNRS UMR5504

description: Dendrislides are prepared according to Trevisiol et al. 2003, New J. Chem. 27,1713-1719.

first: Marlène

last: Cot

first: Jean

last: François

manufacture_protocol: 4x8 pin head, each pin has spotted a block of 20x21spots. Each well is spotted in duplicate.


title: GenoToul/Biopuces operon Yeast 15K 22x22

description:
Dendrislides are prepared according to Trevisiol et al. 2003, New J. Chem., 27, 1713-1719.
This array represents a condensed version of full array.

first: laurent

last: benbadis

first: marlène

last: cot

first: jean

last: françois

manufacture_protocol: 4x8 pin head, each pin has spotted a block of 22x22 spots. Each well is spotted in duplicate.


title: Proteins from vacuoles of Cyanidioschyzon merolae strain 10D

city: Nishiikebukuro

first: Fumi

last: Yagisawa

state: Tokyo

department: Research Information Center for Extremophiles

institute: Rikkyo (St. Paul's) University

organism: Cyanidioschyzon merolae strain 10D

technology: MS

description:
The vacuoles of Cyanidioschyzon merolae strain 10D (Eukaryota; Rhodophyta; Bangiophyceae; Cyanidiales; Cyanidiaceae) synchronized at interphase.
The vacuoles of C. merolae synchronized at interphase were isolated by differential and iodixanol-gradient ultracentrifugation. The supernatant (5 ug of protein) were subjected to SDS-PAGE, cut into 69 slices without staining, and subjected to automatic sample preparation for MALDI-TOF-MS by a robot Xcise (Shimadzu). Alternatively, the vacuolar fraction protein (15.8 ug) was alkylated with 5% (w/v) acrylamide, subjected to SDS-PAGE, and stained with Imperial Protein Stain (Pierce). The gel slices of 58 visible bands were destained and digested as described previously (PMID: 11507753). After the digestion, the peptide fragments were extracted from the gel pieces with 5% (v/v) formic acid in 50% (v/v) CH3CN. Extracts were dried in a vacuum concentrator. The dried peptides were dissolved in 0.1% (v/v) trichloroacetic acid (TFA), desalted using uC18-Zip Tip microcolumns (Millipore) and spotted onto a 384-well plate (KRATOS Analytical). After completely drying the samples, 0.5% (w/v) alpha-cyano-4-hydroxycinnamic acid in 50% (v/v) CH3CN and 0.1% (v/v) TFA were spotted on the peptide spots and allowed to dry. The samples were analyzed by peptide mass fingerprinting (PMF) using a mass spectrometer (AXIMA-TOF2; Shimadzu) in the reflectron mode. When samples could not be identified by PMF, several peptide peaks were further analyzed by post source decay (PSD)-MS/MS. Database searches were performed using the software program MASCOT v2.2.01 (Matrix Science) running on a local database built from the FASTA files of 5014 open reading frames in the C. merolae genome database (http://merolae.biol.s.u-tokyo.ac.jp/). The peptide tolerance was set to 0.1-0.2 Da. Cysteine carbamidomethylation (for samples prepared by Xcise) or propionamidation (for manually prepared samples) was included as a fixed modification and methionine oxidation was included as a variable modification. The identification threshold was set to p < 0.05. As a result, 46 proteins were identified.


title: Hitachi human oligo chip - drug responsive genes

city: Tokyo

first: TERAO

last: KIMIO

address: 2-1-1,Nihombashimuromachi, Chuo-ku

department: Clinicalpharmacology

institute: Chugai Pharmaceutical co.,ltd.

organism: Homo sapiens

first: Kimio

last: Terao

first: Haruki

last: Kinoshita

first: Toshiro

last: Saito

first: Kumiko

last: Kamihara

manufacture_protocol: In this test, Hitachi human oligo chip was used. 8 oligonucleotide probes (80-mer) designed to truly represent human drug responsive genes are spotted on this microarray. The sequences of the probes were designed by using original algorithm developed by Hitachi, Ltd. from the RefSeq as the sequence source. Twenty-four (24) oligos are spotted on the chip.


title: Illumina Genome Analyzer (Candida albicans)

last: GEO

organism: Candida albicans


title: Affymetrix S. cerevisiae TAG4 101K array [condensed version]

city: Berkeley

first: William

last: Jo

address: 119 Morgan Hall

institute: UC Berkeley

description: Preprocessed data format after extraction from raw data file for Affymetrix TAG4 S. cerevisiae array. Original array platform design can be found as raw data file and in submission GPL8633.

first: Alex

last: Loguinov

first: Chris

last: Vulpe

manufacture_protocol: In situ synthesis (Affymetrix)


title: AB SOLiD System 2.0 (Homo sapiens)


title: Nimblegen Pasteurella multocida 2.015 K oligo array

city: Mississippi state

first: Bindu

last: Nanduri

state: MS

address: Box 6100 Spring Street

department: Basic Sciences

institute: Mississippi State University

organism: Pasteurella multocida subsp. multocida str. Pm70

description: The custom oligonucleotide microarray consisting of all the 2015 annotated open reading frames (ORFs) of Pasteurella multocida strain Pm70 was constructed by NimbleGen Systems. The array design included 23 perfect match (PM) and mismatch (MM) probes per target gene, and each probe was spotted twice.

manufacture_protocol: Maskless Array Synthesizer (MAS) technology


title: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain RM1170

status: Public on Aug 04 2009

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Campylobacter jejuni

description: This set includes 6982 oligo nucleotides, has 23232 spots distributed in 48 blocks.

manufacture_protocol: 2QCJ, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: UCSF Homo sapiens CGH 8p11q

city: San Francsico

first: Serena

last: kwek

address: 2340 Sutter St.

department: Cancer Research Institute

institute: UCSF

first: S

last: Kwek

first: D

middle: G

last: Albertson

manufacture_protocol: Isolation of BAC/P1 DNA. We inoculated 0.1ul of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 ug/ml) or kanamycin (50 ug/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37 degrees C with agitation at 225 rpm. We prepared larger cultures for DNA isolation, by inoculating 25 ml  LB media, containing the appropriate antibiotic with 200 ul of the previously grown overnight culture and incubating in a shaking incubator at 37 degrees C at 225 rpm overnight (~16 h). We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm. We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol. We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4 degrees C to pellet the bacteria. We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer’s recommended concentration and then added buffer P2 (1.5 ml). We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min. We inverted each tube once and centrifuged at 4000 rpm at 4 degrees C until the supernatant became clear (45 to 60 min). We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer’s protocol. We followed the manufacturer’s protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65 degrees C before it was added to the column. After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4 degrees C. We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4 degrees C. After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 ul of H2O. We determined the DNA concentration using a fluorometer. The yield typically ranged between 60-100 ng/ul (i.e. 3-5 ug per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel. We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel.  Preparation of BAC/P1 DNA representations by ligation-mediated PCR. We digested the DNA with MseI by incubating overnight at 37 degrees C in a 5 ul reaction containing 1.5 ul DNA (20 to 600 ng), 0.4 U/ul MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham). For ligation of adapters, we diluted 1 ul of each digest to a final concentration of 1 ng/ul with H2O and then mixed 1 ng of the digested DNA with 0.5 ul One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 ul of 100 uM Primer 1 (TAACTAGCATGC), 0.5 ul of 100 uM Primer 2 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 ul H2O. We incubated the mixture at 65 degrees C for 1 min after which we ramped the temperature down to 15 degrees C with a ramp-speed of 1.3 degrees C per minute. When the temperature reached 15 degrees C, we added 1 ul of 10 mM ATP and 1 ul T4-DNA ligase (5 U/ul, Gibco BRL) and continued incubation at 15 degrees C overnight. To initiate the first round of PCR amplification, we added a 40 ul mixture, consisting of 3 ul PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 ul of a mixture of each nucleotide (10 mM) and 35 ul H2O to the ligation reaction. Before we started the PCR program, we incubated the reaction at 68 degrees C for 4 min and then added 1 ul DNA polymerase (3.5 U/ul, Expand Long Template PCR System, Roche). We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.25 min for 14 cycles, followed by, 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.75 min for 34 cycles and 94 degrees C for 40 s, 57 degrees C for 30 s and 68 degrees C for 5 min for the final cycle. We electrophoresed 3.5 ul of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp. To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 ul reaction containing 1 ul of the primary PCR product, 4 uM Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95 degrees C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95 degrees C for 30 s, 50 degrees C for 30 s and 72 degrees C for 2 min for 45 cycles and finally 7 min at 72 degrees C. This reaction yields ~10 ug of DNA, with each fragment containing a 5’ amino linker.  Preparation of DNA spotting solutions. We evaporated the amplification reaction (100 ul) to a final volume of 50 ul by incubation at 45 degrees C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA. (The use of ethanol precipitation proved superior to isopropanol precipitation.) We inverted the tubes and chilled them at –20 degrees C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min. We washed the pellets with 70% ethanol (150 ul) and collected them by centrifugation at 1699 rcf for 45 min. We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 ul of 20% DMSO in H2O (~0.8 ug/ul). We transferred the DNA solutions into 864 well microtitre plates for robotic arraying. Previously, we prepared DNA for spotting in 80% DMSO and 0.3 ug/ul nitrocellulose. However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose. We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5’amino linkers and that spotting solutions made with 20% DMSO performed well. We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior.  Array printing. We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 μm diameter spots on 130 μm centers. We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area. We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs). We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene). We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.


title: Candidatus Pelagibacter ubique OSU_SAR11_affychip

city: Madison

first: Michael

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

manufacture_protocol:
Oligos designed using sequences from three SAR11 genomes (HTCC1062, 1002, 7211) as well as highly similar sequences from the first metagenomic GOS survey (Venter et al. 2004).  No mismatch probes are included on the chip.  All probes target biotin-labeled antisense-RNA.  Probes hard pruned against 16s and 23s rRNA genes.
Affy description of production (from website):
GeneChip microarrays are a classic Silicon Valley innovation, combining several disciplines to create a new technology and more useful research tool. The integration of semiconductor fabrication techniques, solid phase chemistry, combinatorial chemistry, molecular biology, and sophisticated robotics results in a unique photolithographic manufacturing process that produces GeneChip arrays with millions of probes on a small glass chip.
The photolithographic process begins by coating a 5″ x 5″ quartz wafer with a light-sensitive chemical compound that prevents coupling between the wafer and the first nucleotide of the DNA probe being created. Lithographic masks are used to either block or transmit light onto specific locations of the wafer surface. The surface is then flooded with a solution containing either adenine, thymine, cytosine, or guanine, and coupling occurs only in those regions on the glass that have been deprotected through illumination.
The coupled nucleotide also bears a light-sensitive protecting group, so the cycle can be repeated. In this way, the microarray is built as the probes are synthesized through repeated cycles of deprotection and coupling. The process is repeated until the probes reach their full length, usually 25 nucleotides. Commercially available arrays are typically manufactured at a density of over 1.3 million unique features per array. Depending on the demands of the experiment and the number of probes required per array, each quartz wafer can be diced into tens or hundreds of individual arrays.


title: Kyoto University Custom Agilent Ciona intestinails 242K Tiling Array No.1 (of 2)

city: Kyoto

first: Atsushi

last: Kubo

address: Sakyo-ku

institute: Kyoto University

organism: Ciona intestinalis

first: Yutaka

last: Satou

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: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain NCTC_11168


title: Custom GER rice oligoarray

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

organism: Oryza sativa

description:
Oryza sativa subsp. Japonica
Cultivar: Nipponbare

manufacture_protocol:
Probe design: eArray ver 4.5
Array design: eArray ver 4.5


title: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain 81-176

description: This set includes 6982 oligo nucleotides, has 23232 spots distributed in 48 blocks


title: CBCB Listeria monocytogenes 385K v1.0

status: Public on Jul 30 2009

city: College Park

first: Adam

last: Phillippy

address: Biomolecular Sciences Building #296, University of Maryland

department: Center for Bioinformatics and Computational Biology

institute: University of Maryland

organism:
Listeria monocytogenes
Listeria monocytogenes EGD-e
Listeria monocytogenes serotype 4b str. F2365
Listeria monocytogenes serotype 1/2a str. F6854
Listeria monocytogenes serotype 4b str. H7858
Listeria monocytogenes FSL F2-515
Listeria monocytogenes FSL J1-194
Listeria monocytogenes FSL J1-175
Listeria monocytogenes FSL J1-208
Listeria monocytogenes FSL J2-003
Listeria monocytogenes FSL J2-071
Listeria monocytogenes FSL J2-064
Listeria monocytogenes FSL N1-017
Listeria monocytogenes FSL N3-165
Listeria monocytogenes FSL R2-503
Listeria monocytogenes F6900
Listeria monocytogenes J0161
Listeria monocytogenes J2818
Listeria monocytogenes LO28
Listeria monocytogenes 10403S
Listeria monocytogenes HPB2262

description:
This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. The tiled strains by GenBank TaxID are: 265669, 267409, 267410, 393116, 393117, 393118, 393119, 393120, 393122, 393123, 393124, 393125, 393128, 393130, 393131, 393132, 393133, 401650, 393121, 169963.
IMPORTANT: The genomic positions in the data table only represent the position on a single genome. The supplementary files contain the mapping of probes to pan-genomic positions. The columns in the supplementary "probe_mapping" file are:
ID_REF: Probe ID. Each probe can appear in multiple rows depending on how many genomes it targets.
GI_RANGE: Sequence GenBank GI and probe mapping location.
RANGE_STRAND: Strand on the GI sequence the probe maps to.
MISMATCH: Number of mismatches between probe and genomic sequence, 0 or 1.

first: Xiangyu

last: Deng

first: Wei

last: Zhang

first: Steven

last: Salzberg

manufacture_protocol:
Nimblegen 385k CGH HD2 Array: http://www.nimblegen.com/products/lit/cgh_hd2_datasheet_2008_04_07.pdf
Nimblegen Protocols: http://www.nimblegen.com/products/lit/cgh_userguide_v5p1.pdf


title: FHCRC Yeast ORF 6K Array

city: Seattle

first: lihong

last: li

address: 1100 Fairview Ave N.

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

organism: Saccharomyces cerevisiae

manufacture_protocol: Yeast ORFs are spotted on the array.


title: SCKCEN Rhodospirillum rubrum ATCC 11170 Genomic Array

status: Public on Jan 01 2009

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

organism: Rhodospirillum rubrum ATCC 11170

first: Felice

last: Mastroleo

first: Rafi

last: Benotmane

first: Max

last: Mergeay

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


title: Agilent-014947 microRNA array (early access version)

city: Beppu

first: Takehiko

last: Yokobori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

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


title: JCVI Pseudomonas fluorescens Pf-5 23k v1.0

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

organism: Pseudomonas protegens Pf-5

technology: mixed spotted oligonucleotide/cDNA

first: Joyce

last: Loper

first: Katherine

first: Daniel

last: Johnson

manufacture_protocol: Unique 70-mer oligonucleotides were designed for 6147 genes of the Pseudomonas fluorescens Pf-5 genome. Oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented three times on the array. Negative controls include 50% DMSO / 50% DI water and air. Arabidopsis spike-in controls and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.


title: JCVI Pseudomonas fluorescens Pf-5 28k v2.0

manufacture_protocol: Unique 70-mer oligonucleotides were designed for 6147 genes of the Pseudomonas fluorescens Pf-5 genome. Oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented four times on the array. Negative controls include 50% DMSO / 50% DI water and air. Arabidopsis spike-in controls and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.


title: GenoToul/Biopuces operon_yeast22x22 (2003)

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

institute: INSA

description: Dendrislides are prepared according to Trevisiol et al. 2003, New J. Chem. 27, 1713-1719

first: Klaudia

last: Kuranda

first: Véronique

last: Le Berre

first: Jean-Marie

last: François

manufacture_protocol:
4x8 pin head, each pin has spotted a block of 22x22 spots.
Each well is spotted in duplicate.


title: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain RM1221

first: PFGRC

last: JCVI

state: MD


title: TIGR Myxococcus xanthus oligo array 7.2K

status: Public on Aug 26 2009

city: Marburg

first: Penelope

last: Higgs

address: Karl-von-Frisch-Str.

department: Ecophysiology

institute: Max Planck Institute for Terrestrial Microbiology

organism: Myxococcus xanthus

manufacturer: The Institute for Genomic Research (TIGR)

first: Frank-Dietrich

last: Müller

manufacture_protocol: Spotted DNA 70-mers


title: JCVI PFGRC Campylobacter jejuni 23K v2 array designed primarily based on strain 269.97

description: This set includes 6982 oligonucleotides, has 23232 spots distributed in 48 blocks.