title: CAG Human 19k array v1.0

status: Public on Jun 01 2006

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

country: USA

institute: PHRI-UMNDJ

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: non-commercial

first: Patrica

last: Soteropoulos

first: Tongsheng

last: Wang

first: Saleena

middle: S

last: Ghanny

manufacture_protocol: Compugen Human OligoLibraryTM, 2001.  60-mer oligonucleotides in a 3x SSC solution are printed on Poly-L-Lysine coated glass slides with 48 TeleChem SMP3 pins on a GeneMachines OmniGrid 100 Microarrayer.  Slides are post processed by rehydrating, snap drying, UV crosslinking (600x100 microjoules of energy), and blocking with Succinic Anhydride.


title: LICR/UCSD RenLab Hu6K array

status: Public on Apr 21 2005

city: San Diego

first: Chunxu

last: Qu

state: CA

department: Gene Regulation

institute: Ludwig Institute for Cancer Research

technology: spotted DNA/cDNA

description: Overexpression of c-Myc is one of the most common alterations in human cancers, yet it is not clear how this transcription factor acts to promote malignant transformation. To understand the molecular targets of c-Myc function, we have used an unbiased genome-wide location-analysis approach to examine the genomic binding sites of c-Myc in Burkitt's lymphoma cells. We find that c-Myc together with its heterodimeric partner, Max, occupy >15% of gene promoters tested in these cancer cells. The DNA binding of c-Myc and Max correlates extensively with gene expression throughout the genome, a hallmark attribute of general transcription factors. The c-Myc/Max heterodimer complexes also colocalize with transcription factor IID in these cells, further supporting a general role for overexpressed c-Myc in global gene regulation. In addition, transcription of a majority of c-Myc target genes exhibits changes correlated with levels of c-myc mRNA in a diverse set of tissues and cell lines, supporting the conclusion that c-Myc regulates them. Taken together, these results suggest a general role for overexpressed c-Myc in global transcriptional regulation in some cancer cells and point toward molecular mechanisms for c-Myc function in malignant transformation.

first: Zirong

last: Li

first: Sara

last: van Calcar

first: Webster

middle: K

last: Cavenee

first: Michael

middle: Q

last: Zhang

first: Bing

last: Ren


title: Affymetrix GeneChip Rat Expression Set 230 Array RAE230A PM probes

status: Public on Jun 30 2006

city: Mannheim

first: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

organism: Rattus norvegicus

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: PM probes of the Affymetrix GeneChip Rat Expression Set 230 Array RAE230A


title: Human UniGene Set RZPD 1

status: Public on Jul 08 2003

city: Kiel

first: Nancy

last: Mah

institute: Christian-Albrechts-University Kiel

description:
Preparation of high density cDNA arrays.

cDNA clone inserts (not sequence-verified) from eighty-eight 384-well microtitre plates from the Human Unigene 1 clone set (RZPD Deutsches Ressourcenzentrum für Genomforschung
and Boer et al. 2001) and a custom-made plate of an additional 258 clones (sequence-verified) were amplified by PCR in a 384-well format using M13 forward (5`-CGTTGTAAAACGACGGCCAGT-3´) and reverse (5´-TTTCACACAGGAAACAGCTATGAC-3´) primers.  The PCR reaction was set up by dipping a 384-pin replicator (Genetix, UK) twice into the bacterial library plate and transferring the solution (approximately 0.2 µL) to a new PCR plate containing 25µL of PCR master mix in each well (final concentrations: 1 X PCR buffer (0.5M Tris-HCl (pH 8.6), 0.5M KCl, 15mM MgCl2, 1% Tween 20), betaine (1.5U), 0.2mM dNTPs, 0.2mM primers and 0.1U/µL Taq/Pfu).  Amplification of PCR products was carried out as follows:  95ºC for 1 min, 94ºC for 15 sec, 59ºC for 15 sec, 65ºC for 55 sec, repeat of 59ºC for 15 sec, 65ºC for 55 sec for an additional 2 cycles, repeat of 94ºC for 15 sec, 59ºC for 15 sec, 65ºC for 55 sec for 29 cycles and finally 68ºC for 10 min.  The sub-cycling step described improved product yield and stability.  The quality of the PCR reaction was determined visually by slot-blot electrophoresis on 1% agarose gels.

Prior to spotting, PCR products were denatured by the addition of a final concentration of 0.1M NaOH to each well.  The ~34,000 PCR products were repeatedly spotted 7 times in a 6 X 6 pattern (asymmetrically to ensure ease in determining filter orientation) on dry 23 X 23 cm Hybond N+ nylon membranes (Amersham Pharmacia) using a Genetix robot attached to a 384 pin gadget-head (250 mm pins).  The 6 X 6 spotting blocks were organized into six fields of 384 spotting blocks (arranged 16 X 24), resulting in 2304 spotting blocks on each filter. Each 6 X 6 spotting block contained duplicate PCR products from 15 clones (14 clones in field 6), duplicate Arabidoposis thaliana clones (GenBank accession numbers AF104328 and U29785, derived from the Arabidopsis Biological Resource Center and DNA stock donor at Ohio State University) serve as guide spots during subsequent gridding steps, and four (six in field 6) empty positions to allow for an estimation of background intensity after hybridization.  In order to determine the quality of the spotting, 1.58 µM fluorescin was added to the Arabidoposis thaliana control clone plate and the filter was scanned using an ‘in-house’ work station for high resolution fluorescence detection (MPI for Molecular Genetics, Berlin).  In this way, unevenly or poorly spotted filters were discarded prior to hybridization.  After spotting, cDNA on the filters was further denatured by floating filters (face up) in 0.4M NaOH for 2 min and neutralized with 5 X SSC (pH 7.5) for 2 min.  The DNA was cross-linked to the filter by heat-baking at 80°C for 30 min and exposing to ultraviolet radiation (Stratalinker UV cross-linker (auto cross-link option); Stratagene).  Filters were stored dry at 4°C until ready for use.

Reference:
Boer, J.M., Huber, W.K., Sultmann, H., Wilmer, F., von Heydebreck, A., Haas, S., Korn, B., Gunawan, B., Vente, A., Fuzesi, L. et al. (2001) Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500- element cDNA array. Genome Res, 11, 1861-1870.

first: Christine

middle: M

last: Costello

first: Brigitte

last: Mauracher

first: Georg

last: Waetzig

first: Holger

last: Eickhoff

first: Stefan

last: Schreiber

first: Hans

last: Lehrach


title: DrosophilaWhiteLabNov2001

status: Public on Jan 31 2003

city: Cambridge

first: Scott

middle: A

last: Rifkin

state: MA

address: 16 Divinity Ave

department: OEB

institute: Harvard University

organism: Drosophila melanogaster

description: Drosophila melanogaster PCR fragment arrays, TRLi2Plates1600 w/tp, Nov2001 format


title: SHDJ

status: Public on Jan 12 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine

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


title: NKI/VanSteensel_HSAP_390k_2005-08-15_Vogel_human

status: Public on Jun 25 2006

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Non-repetitive part of Human Chromosome 19, ENCODE regions, Promoters, Ultraconserved elements,
Based on Human genome sequence NCBI 35.

first: Elzo

last: de Wit

first: Maartje

middle: J

last: Vogel

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


title: Whole Genome, Alternative Splicing Drosophila Chip v3

status: Public on Jun 06 2006

city: Gainesville

first: Lauren

middle: M.

last: McIntyre

state: FL

department: Dept. of Molecular Genetics and Microbiology

institute: University of Florida

manufacture_protocol: Oligonucleotide probes were designed using an approach that utilized the sequences of transcripts without incorporating any a priori knowledge about their exon/intron


title: RIKEN human 21K array

status: Public on Oct 28 2004

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description:
This array was made in the laboratory of Dr. Yasushi Okazaki at the Riken Genome Science Center, Yokohama Institute in Japan. The array contains 21,168 spots including 20784 spots of human cDNA clones purchased from ResGen™ (Invitrogen Corporation, Carlsbad, CA, USA) and the remaining spots are the internal and exogenous controls spotted on every subgrid as positive and negative controls.
Keywords = RIKEN human 21K cDNA

last: Otani

first: Megu

last: Ohtaki

first: Kenichi

last: Satoh

first: Yasushi

last: Okazaki

first: Yoshihide

last: Hayashizaki

first: Keiji

last: Tanimoto

first: Masahiko

last: Nishiyama


title: STv2_MMCC

status: Public on Mar 16 2003

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

description: Custom made Salmonella array

first: Steffen

last: Porwollik

first: Jonathan

middle: G

last: Frye

first: Felisa

last: Blackmer


title: MSU-4_01-02

status: Public on Aug 06 2004

first: Shuang

last: Chang

state: MO

department: Biology

institute: Washington University

organism: Arabidopsis thaliana

description:
Tip Configuration: Standard 48 tip
Columns per Sector: 18
Rows per Sector: 18
Column Spacing: 230
Row Spacing: 230


title: Candida_albicans_ArrayII

status: Public on Jun 29 2006

city: Boston

first: Anna

last: Selmecki

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

organism: Candida albicans

manufacture_protocol: Primer pairs were used to amplify Candida albicans ORFs from SC5314 genomic DNA.  PCR fragments were purified on  MultiScreen-PCR 96-well filtration units (Millipore, Bedford, Mass.) and were eluted in spotting buffer (3 SSC [(1 SSC is 0.15 M NaCl plus 0.015 M sodium citrate] plus 0.01% SDS). Purified PCR products were spotted in duplicate on poly-L-lysine-coated slides with a MicroGrid II (BioRobotics, Cambridge, United Kingdom). Slides were postprocessed with succinic anhydride in 1-methyl-2-pyrrolidinone (http://www.microarrays.org/protocols.html).


title: elegans_Fprint_YMD

status: Public on Jun 13 2006

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

organism: Caenorhabditis elegans

description: 6th print of sjj primer 1st PCR

manufacture_protocol: proprietary


title: elegans_Cprint_YMD

description: the third print run at Yale using the 1st PCR of the sjj primer set


title: Streptococcus pneumoniae TIGR4/R6 v2

status: Public on Jun 24 2006

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

institute: University of Groningen

organism: Streptococcus pneumoniae

manufacturer: Department of Molecular Genetics, Groningen, the Netherlands

first: Anne

last: de Jong

manufacture_protocol: Amplicons were designed using GenomePrimer in combination with UniFrag, amplified by Eurogentec (Belgium), purified using Qiagen 96-wells purifying plates. Amplicons (about 10 microL) diluted 2x with ArrayIT 2x spotting buffer, in Genetix 384 wells spot plates, spotted on aminosilane slides (EZ-Ray) with a GenPak spotter at about 55 % humidity. Amplicons were cross-linked to the glass slide surface by UV-treatment. Slides were cleaned by boric anhydride treatment.


title: Agilent/Paradigm Arabidopsis 60mer in situ Genome Array

status: Public on Oct 09 2003

city: RTP,

first: Yang

last: Qiu

state: NC

address: 108 TW Alexander Dr.

department: Investigational Genomics

institute: Paradigm Genetics, Inc

description: This array contains 20,426 Arabidopsis thaliana gene probes as specified by Paradigm Genetics. It is manufactured by Agilent Technologies by in situ synthesis of 60mer oligonucleotides using an ink-jet printing method.


title: FG002 Genomic Tiling Array

status: Public on Jun 20 2006

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

first: Lisa

last: Meadows

first: Richard

last: Auburn

first: Bettina

last: Fischer

first: Shan

last: Gao

first: Edward

last: Ryder

first: Robert

last: White

first: Steven

manufacture_protocol:
PCR amplicon tiling array from Drosophila genomic DNA.  Primers as described for GEO platform GPL1918.
Double stranded DNA amplified from Drosophila genomic DNA.
Spotted on FMB-cDNA slides
Printing protocols available at http://www.flychip.org.uk


title: Candida_albicans_ArrayI


title: TJUDBI Rat 3K

status: Public on Jun 21 2006

city: Philadelphia

first: Gregory

last: Miller

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

first: Daniel

middle: E

last: Zak

first: Hester

last: Liu

first: James

last: Schwaber

manufacture_protocol: Described in Zak et al 2006 (Pubmed ID 16784547)


title: Nimblegen Human 5K promoter array 2

city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

manufacture_protocol: tiling array


title: DGRC-D. melanogaster-DGRC1-15552-v3

status: Public on Jun 02 2006

city: Bloomington

last: Drosophila Genomics Resource Center (DGRC)

state: IN

department: Indiana University

description: DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics.  The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP.  The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides.

first: Justen

last: Andrews

first: Peter

last: Cherbas

first: Kevin

last: Bogart

first: Monica

last: Sentmanat

first: Jim

last: Costello

first: Angela

last: Burr


title: DGRC-D. melanogaster-DGRC1-15552-v1

institute: Drosophila Genomics Resource Center (DGRC)

description: DGRC-1 amplicon transcriptome microarrays  are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics.  The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP.  The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides.


title: Research Genetics  (Invitrogen) GF200 microarray filter

status: Public on Jun 28 2006

city: Tampere

first: Kati

middle: Marjaana

last: Juuti-Uusitalo

address: Biokatu 10

department: Medical School

country: Finland

institute: Pediatric Research Center

description: Research genetics GF200 nylon membrane containing 5184 spotted cDNA clones

manufacture_protocol: see manufacturer's web site


title: Operon-Compugen array

status: Public on Jun 01 2006

first: Winston

middle: Patrick

last: Kuo

address: 188 Longwood Avenue

institute: Harvard Medical School

organism: Mus musculus

middle: P

manufacture_protocol: The 16K mouse oligonucleotide arrays were inkjet-printed by the microarray facility at California Institute of Technology. This oligonucleotide array consists of 13,536 probes of 70mers (Operon Technologies Inc., Alameda, CA) and 2,304 probes of 65mers (Sigma-Genosys, The Woodlands, TX).


title: DGRC-D. melanogaster-DGRC1-15552-v4

manufacturer: Drosophila Genomics Resource Center (DGRC)


title: DGRC-D. melanogaster-DGRC1-15552-v2


title: GE-Amersham-CodeLink-10K

description: CodeLink UniSet Mouse I Bioarray contains single-stranded oligonucleotide probes derived from a large majority of publicly available, well-annotated mRNA sequences found in the Mouse UniGene set of unique clusters. Each bioarray contains probes for an independent assay of all 10,000 genes in the set. This is the old version.


title: Streptococcus pneumoniae TIGR4/R6 v3

first: Sacha

last: van Hijum

manufacturer: Department of Molecular Genetics, university of Groningen, the Netherlands

first: Anne

last: de Jong


title: Cotton LSL Array

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism: Gossypium hirsutum

description: 1942 spot Late Season Cotton Leaf ESTs cDNA

first: Ranamalie

last: Amarasinghe

first: Danny

last: Llewellyn

manufacture_protocol: The cDNA clones from the late-season leaf cDNA library were PCR amplified and printed onto CMT-GAPS coated microarray slides (Corning) using a VersArray ChipWriter Pro arrayer (Bio-Rad, Hercules, CA) as described in Wu et al., (2005). Post-printing slide processing was performed by baking the slides at 80oC for 3 hours as described in the manufacturer's technical manual.


title: MWG BIOTECH 11K ARRAY

manufacture_protocol: Briefly, RNA was prepared using the RNeasy Midi kit according to the manufacturer's instructions (Qiagen). First-strand complementary DNA synthesis from 5ug total RNA was done at 42oC for 1h, followed by second-strand cDNA synthesis at 16oC for 2h. RNase I digestion was followed by proteinase K treatment. The resulting double-stranded cDNA was purified using the RNeasy Mini Kit according to the manufacturer's instructions (Qiagen). Fluorescence-labeled RNA was generated by carrying out an in vitro transcription reaction (40 mM Tris-HCl, pH 7.5, 7 mM MgCl2, 10 mM NaCl, 2 mM spermidine, 5 mM ditihothreitol, 7.5 mM each of ATP, CTP and GTP, 5 mM UTP, 20 units RNase inhibitor and 1,000 units T7 polymerase) at 37oC for 4h. This reaction was done in the presence of fluorescence-labeled nucleotide (Amersham Pharmacia Biotech) to generate Cy3- or Cy5-labelled RNA. The labeled RNA was subsequently purified (Qiagen RNeasy Mini kit) and chemically fragmented at 94oC for 15 min in fragmentation buffer (20 mM Tris-acetate, pH8.1, 50 mM potassium acetate, 15 mM magnesium acetate). The fragmented, Cy3- or Cy5-labelled complementary RNA (20ug) was lyophilized, resolubilized in hybridization buffer (50% formamide, 50mM sodium phosphate, pH8.0, 6X SSC, 5X Denhardt's Solution, 0.5% SDS), and hybridized to oligonucleotide mouse 11K microarrays at 42oC for 24h. T7 RNA polymerase was purchased from Ambion: primers, RNase inhibitors and all other enzymes were purchased from Roche Molecular Biochemicals.


title: UCSF Mus musculus 39K 15Mm MEEBO Oligo Array

city: San Francisco

first: Agnes

last: Paquet

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: Arrays were printed on aminosilane coated slides (Schott Nexterion, Elmford, NY)

first: Andrea

last: Barczak

first: Rebecca

last: Barbeau

middle: C

first: David

last: Erle

manufacture_protocol:
More information on the MEEBO oligonucleotides can be found at the Stanford Alizadeh lab website

Printing instructions can be found here:

Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ. Spotted long oligonucleotide arrays for human gene expression analysis.
Genome Res. 2003 Jul;13(7):1775-85. Epub 2003 Jun 12.
PMID: 12805270


title: DNA_Tags_3

status: Public on Jun 15 2006

city: New Orleans

first: Timothy

last: Hammond

state: LA

address: 1430 Tulane Ave

department: Department of Medicine, Nephrology Section, SL-45

institute: Tulane University Health Sciences Center

organism: Saccharomyces cerevisiae

description: The TAG3 array contains oligonucleotide sequences used to detect the "barcode" sequences replacing each ORF in the Saccharomyces cerevisiae deletion series

manufacture_protocol: Affymetrix standard procedures


title: Drosophila melanogaster detoxification array

status: Public on Jun 16 2006

city: Sophia-Antipolis

first: Gaelle

last: LE GOFF

address: 400 route des Chappes

country: France

institute: INRA

description: This “Drosophila toxicology microarray” contained 319 genes that represent all cytochromes P450, glutathione S-transferases, esterases, other genes of interest including attacin or Ftz-F1 and several housekeeping genes as controls.

manufacturer: Plateforme transcriptome INRA-CNRS-UNSA Sophia-Antipolis

first: René

last: Feyereisen

first: Claire

last: Conrad

first: Frédérique

last: Hilliou

first: Naïma

last: Kebdani

first: Charles

last: Robin

first: Cécile

last: Sabourault

first: Luc

last: Sofer

first: Nathalie

last: Tijet

manufacture_protocol: A cDNA microarray was constructed using expressed sequence tags (ESTs) of 1.8 kb average length and gene specific tags of 0.4 kb average length obtained by PCR amplification and plasmid cloning. Each insert was amplified by PCR with flanking universal primers, purified and then spotted using the ChipWriterPro Virtek (BioRad) spotter at three independent locations on Corning UltraGAPS slides (Corning)


title: Valencia yeast v3

status: Public on May 17 2006

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Nylon macroarray (7 x 11 cm) with 6049 single spotted yeast ORF probes. Probes are PCR fragments comprising the whole ORF (5598 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).

first: JE

first: J

last: Garcia-Martinez

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206


title: VC-oligos

status: Public on Dec 15 2005

city: Stanford

first: Melanie

last: Blokesch

address: 279 Campus Drive

institute: Stanford University

organism: Vibrio cholerae

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


title: Hopital Lariboisiere Lab-Arraytor human 500-1 cDNA

status: Public on Jun 27 2006

city: Paris

first: Didier

last: Payen de la Garanderie

address: 2 rue Ambroise Pare

department: DAR-ICU

institute: Hopital Lariboisiere

manufacture_protocol:
Lab-Arraytor® human 500-1 cDNA arrays are manufactured using a robot-based high-speed
contact spotting facility which ensures high precision positioning and constant droplet
volumes of cDNA samples to provide an reproducible spot morphology
and DNA content over the whole array. The process is performed under dust free, temperature-
and humidity controlled conditions. The spotted cDNA is covalently bound to
the glass surface. The array quality is meticulously controlled by relevant staining and
hybridization procedures.


title: Nimblegen Mouse custom array

status: Public on Jun 06 2006

first: Sharon

last: Squazzo


title: UHN Human 19K EST array

city: Pune

first: Sanjeev

last: Galande

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

first: Chandan

last: Kumar

manufacture_protocol: Spotted cDNA microarray


title: CGH-CHROM14 2K 1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
The array contains 1511 distinct BAC and PAC sequences.The bacs were printed in 2 replicates. 289 BACS are from the Sanger institute. 384 BACS were provided by K.U.Leuven Department CME (Belgium).
838 BACS from chromosome 14 are from the Human 32K BAC rearray of CHORI BACPAC resources. The bacs were amplified by DOP - PCR. In total the array design contains 3840 features printed in a layout of
12 meta rows, 4 meta columns, 8 rows per block and 10 columns per block.

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

first: Guy

last: Froyen

manufacture_protocol:
Equipment:

1. Lucidea microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3.  Motorola slides

Printing at 22176 spot density:
1. Set spotter settings : 55% humidity, column pitch = 400 um, row pitch = 400 um.
2. Make sure room temperature is between 20-24 degrees Celsius.
3. Place microtiter plates in the plate hotel with A1 in upper right corner.
4. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
5. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
6. Slides can be stored for at least 6 months in a dry-cabinet.


title: elegans_Dprint_YMD

first: Valerie

last: Reinke

address: 333 Cedar St

institute: Yale University School of Medicine

description: fourth print of sjj primer set 1st PCR

manufacture_protocol: proprietary


title: Erwinia chrysanthemi Ech3937 array

city: LUBBOCK

first: Michael

last: San Francisco

state: TX

address: Flint and Main St

department: Biological Sciences

institute: Texas Tech University

organism: Dickeya chrysanthemi

description: 4900 Ech genes from

manufacture_protocol: spotted oligonucleotide onto Corning GAPS II


title: Nimblegen Human ENCODE array


title: UCSF Madhani S. cerevisiae ORFarray v2

first: Rachel

last: Tompa

department: Biochemistry

institute: UC San Francisco

manufacture_protocol: Microarrays were fabricated as described (DeRisi et al., 1997, Science 278:680-686. Nearly all annotated S. cerevisiae ORFs were amplified by PCR and spotted onto poly-L-lysine coated glass slides using a robot custom-buit by Dr. Joseph DeRisi (UCSF). Detailed protocols are available at the DeRisi lab website at UCSF.


title: Cepko BMAP cDNA

city: Boston

first: Winston

last: Kuo

description:
E. coli containing the retinal library cDNA inserts were inoculated into 96 deep well blocks containing 1.2 ml of 2xYT media using disposable plastic replicators (Genetix, Hampshire, UK). Cultures were grown at 37°C for 20 hours under constant shaking at 200 RPM and finally pelleted via centrifugation. Plasmids were purified using the QIAprep Turbo kit (Qiagen, Valencia, CA, USA). 96 pin disposable replicators were used to transfer plasmid templates to PCR plates containing 60 ?l of reaction mix. PCR reactions utilizing M13 forward and reverse primers and Taq polymerase (Qiagen) underwent 32 cycles of 95°C for 45 seconds, 53°C for 45 seconds, and 72°C for 2:45. PCR products were purified using QIAquick Kit (Qiagen) and eluted in 100 ?l of water. PCR products were quality scored and sized by running on a 2% agarose 96 well E-gel (Invitrogen Corporation, Carlsbad, CA). Products ranged in size from 300 bp to 3000 bp. The total PCR yield for each well was measured on a SPECTRAmax PLUS spectrophotometer (Molecular Devices, Sunnyvale, CA). Plates containing less than 1.5 ?g of product were reamplified and combined until the total mass exceeded this value. Plates were dried at room temperature, resuspended in 50 ?l of water, and transferred to 384 well V-bottom spotting plates (Genetix).

Spotting plates were dried at room temperature and products were resuspended in 7.5 ?l of 30% DMSO (Sigma-Aldrich, St. Louis, MO, USA) A Biorobotics MicroGrid TAS II with 16 Microspot 10K quill pins (Genomic Solutions, Ann Arbor, MI, USA) was used to array PCR products at a pitch of 260 ?m onto UltraGAPS amino-silane coated slides (Corning, Corning, NY, USA) in a relative humidity of 45% ± 2%. Microarrays were rehydrated in a humidity chamber for 30 seconds, denatured on a heat block at 95°C for 30 sec, and ultimately crosslinked at 125 mJ in a GS Genelinker UV chamber (Biorad, Hercules, CA, USA). Slides were blocked for 1 hour with a 50% formamide, 5x SCC, 0.1% SDS, 0.1 mg/ml BSA solution.

manufacture_protocol: Mouse retinal cDNA clones were assembled from four different libraries generated by M.B. Soares (Bonaldo, Lennon et al. 1996). NIH_BMAP_Ret1 is a normalized library derived from embryonic retina tissue and comprises 9.8% of the collection. NIH_BMAP_Ret2 is a normalized library derived from neonatal retina tissue and comprises 8.8% of the collection. NIH_BMAP_Ret3 is a normalized library derived from adult retina tissue and comprises 8.6% of the collection. NIH_BMAP_Ret4 is a subtracted library derived from retinal tissue at various stages of development and comprises 72.8% of the collection.


title: L vannamei microarray 2005

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

organism: Penaeus vannamei

manufacturer: Hollings Marine Laboratory, Genomics Core

first: Javier

last: Robalino

last: Gross

first: Joan

last: Colglazier

first: Megan

middle: T

last: Peck

first: Robert

middle: W

last: Chapman

first: Greg

last: Warr

manufacture_protocol: contact spotting of L. vannamei cDNA clones using a Q-ArrayMax (Genetix) machine, baked for 2 h at 80 ºC, and stored under vacuum until used


title: UI Squid EST 30K cDNA array

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

organism: Euprymna scolopes

description: Glass slide with 30,005 spots (13,978 unique cDNA clone inserts) in 48 blocks consisting of 25 columns and 25 rows.  Blocks are arranged in 12 rows and 4 columns.  The set of 13,978 cDNA clone inserts was identified form the University of Iowa EST collection.  The clone inserts were amplified with T7 and T3 primers and printed with 50% DMSO on UltraGaps slides (Corning) using a ProSys 5510 Microarray Printer.

first: Irina

middle: V

last: Koroleva

first: Einat

last: Snir

first: Hakeem

last: Almabrazi

first: Thomas

middle: L

last: Casavant

first: Marcello

middle: B

last: Soares

first: M

last: McFall-Ngai

manufacture_protocol: The clone inserts were amplified directly from bacterial cell cultures with T7 and T3 primers, purified, dried, resuspended in water and printed with 50% DMSO on UltraGaps slides (Corning) using a ProSys 5510 Microarray Printer.  The 16 control spikes were printed by each pin, at the beginning or at the end of the pin printing area.  The spotted slides were cross-linked and stored in a desiccator.


title: Nimblegen Streptococcus pyogenes  M1 serotype SF370 strain 2.5k

city: Kansas City

first: Alexander

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

organism: Streptococcus pyogenes

manufacture_protocol: The platform was done according to Maskless Array Synthesizer (MAS) technology


title: SuperArray GEArray Q series Human Chemokines and Receptors Gene Array cat. #HS-005

status: Public on Apr 06 2004

city: Frederick

first: SuperArray

last: Bioscience Corporation

state: MD

address: Suite 101, 7320 Executive Way

institute: Technical Support

description:
GEArray Q series Human Chemokines and Receptors Gene Array contains 77 chemokine and chemokine receptor genes. The regulation of chemokine and chemokine receptor expression plays fundamental roles in the development, homeostasis, and function of immune system. It is also evident these genes function in other cell types, such as endothelial cells and cells of the nervous system. Through a simple side-by-side hybridization, you can determine simultaneously the expression profile of these chemokine and chemokine receptor genes by using your experimental RNA samples and the arrays and reagents provided in the kit.
Catalog number HS-005
Platform_weblink: http://www.superarray.com/home.php

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: QIMR Schistosoma 22k oligonucleotide array

status: Public on May 30 2006

city: Forest Hill

first: Russell

middle: Leigh

last: McInnes

state: Vic

address: 347 Burwood Hwy

department: LSCA

institute: Agilent Technologies

organism:
Schistosoma japonicum
Schistosoma mansoni

description: This microarray contains 19,221 non-control 60-mer probes designed to sequences sourced from the Chinese sequencing team (http://schistosoma.chgc.sh.cn/) as of Dec 2004 and from the TIGR Schistosoma mansoni Gene Index (SmGI) release 5.0.  Agilent's 22k control grid with eQC targets is also implemented.

first: Geoff

last: Gobert

first: Don

last: McManus

first: Luke

last: Moertel

first: Nelson

last: Charles

first: Jones

last: Malcolm

first: Hu

last: Wei

manufacture_protocol: Agilent in situ inkjet