title: Custom Agilent C. elegans expression microarray

status: Public on Feb 29 2012

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

organism: Caenorhabditis elegans

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: Standard Agilent Protocol


title: ARK-Genomics Bovine 14K cDNA array

status: Public on Jun 06 2013

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

country: Italy

institute: University of Tuscia

organism: Bos taurus

technology: spotted DNA/cDNA

manufacture_protocol: See manufacturer's web site (http://www.ark-genomics.org/).


title: Custom Agilent C. briggsae expression microarray

organism: Caenorhabditis briggsae


title: Nimblegen Human high-density promoter array CpG island methylation array

status: Public on Sep 26 2012

city: Kiel

first: Zhe

last: Feng

address: Schittenhelmstr. 12

country: Germany

institute: Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany

organism: Homo sapiens

description:
Annotation in this record based on NCBI human build 36. The supplementary files are based on HG18.
Genomic regions of methylation, Iso-thermal (Tm=76) tiling design for ~30k regions from UCSC HG18 at a 82bp interval. Design includes random GC probes.  Additional control probes from non-human sequences provided by customer were tiled at a 10bp interval and included in a separate container. Our microarray consists of 385,574 50-bp probes. the array contained 50-bp probes tiled at ∼100 bp density across the entire human Major Histocompatibility Complex, and promoters and nonpromoter CpG islands on the whole genome. The array was originally designed using the NCBI build 36 version of the human genome assembly.

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


title: Custom Agilent C. brenneri expression microarray

organism: Caenorhabditis brenneri


title: Custom Agilent C. remanei expression microarray

organism: Caenorhabditis remanei


title: Custom Agilent C. japonica expression microarray

organism: Caenorhabditis japonica


title: NimbleGen Staphylococcus aureus NCTC 8325 X4 expression array [DesignID:11374]

city: Leeds

first: Victoria

last: Ryder

state: West Yorkshire

address: Clarendon way

department: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

organism: Staphylococcus aureus subsp. aureus NCTC 8325

description:
Design_ID: 11374
native array description file: 100210_S_aur_8325_WG_expr.ngd
native array description file: 100210_S_aur_8325_WG_expr.ndf

manufacture_protocol: X4 expression array for Staphylococcus aureus NCTC 8325, GenBank NC_007795, 2892 CDS features; 45-60mer probes, 8 probes per target, 2887 exemplars; 3 copies on the array, empty features filled with randomly generated probes of comparable G+C content and length


title: Van Andel Institute Human 18k cDNA microarray

status: Public on Feb 27 2012

city: East Lansing

first: Xuewei

last: Wang

address: 2527 Engineering building, Michigan State University

country: USA

institute: Michigan State University

description: cDNA microarray Van Andel Institute for Day2 sample

distribution: non-commercial

first: Christina

last: Chan

manufacture_protocol: Per Van Andel Institute protocols.


title: SHDP

status: Public on Jan 11 2006

city: Stanford

last: Stanford Microarray Database

state: CA

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: Agilent/INRA FH Sus scrofa 15K muscle array

city: Rennes

first: Frederic

last: Herault

country: France

institute: INRA

organism: Sus scrofa

description:
A custom repertoire of 15,000 60-mer DNA probes targeting transcripts expressed in growing pig skeletal muscle.
This repertoire was print on a multiplex microarray format : 8-plex microarray (eight individual 15K microarrays printed on a single slide)

first: Marie

last: Damon

last: Hérault

first: Pierre

last: Cherel


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array [Custom CDF: ATH1-121501.TAIR10]

status: Public on Mar 08 2012

city: Austin

first: David

middle: Lee

last: Des Marais

state: TX

address: 1 University Station C0930

department: Integrative Biology

institute: The University of Texas at Austin

organism: Arabidopsis thaliana

description: custom CDF file based on TAIR10 annotation.

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: CombiMatrix 90K Petunia axillaris array

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

institute: University of Verona

organism: Petunia axillaris

description: 27,594 specific oligos (35-40mer) were designed on Petunia axillaris tentative consensus (TC) sequences (JI332784-JI359154), and by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls, nine bacterial oligonucleotides sequences provided by CombiMatrix were utilized. The 90K TomatArrayTM 1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by CombiMatrix protocols available at the CombiMatrix website (www.combimatrix.com).

manufacturer: University of Verona -Department of Biotecnology- Plant Functional Genomics Centre

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by CombiMatrix Corporation (Mukilteo, USA) using the CombiMatrix CustomArray synthesizer. Standard synthesis protocol provided by CombiMatrix was used.


title: CUST-40K-Staphylococcus_epidermidis_RP62A

status: Public on Feb 28 2012

city: Houston

first: Mohan

last: Pammi Venkatesh

address: One Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

organism: Staphylococcus epidermidis RP62A

description:
in situ synthesized oligonucleotide microarray
Custom 40K Staphylococcus epidermidis RP62A MYcroarrays and each slide has one array composed of 40,960 spots

manufacture_protocol: In situ synthesized oligonucleotide microarrays were manufactured by MYcroarray and probe sequence designed using a proprietary version of OligoArray 2.0 (25). Arrays were synthesized on slide-sized glass substrates and each slide had one array composed of 40,962 spots, of which 33,715 spots contain 45mer probes for S. epidermidis genes, 525 empty features without a probe and 720 features with MYcroarray quality control probes. In addition, there are 6000 probes for randomly selected Candida genes to assess potential cross hybridization with S. epidermidis genes. There were up to 3 probes per gene and 5 identical replicates of each S. epidermidis probe. Multiple probes per gene format was chosen to account for the genetic variability between S. epidermidis 1457 strain used in our experiment compared to strain RP62A used in the microarray probe design. Also, to avoid theoretical cross contamination, S. epidermidis probes were blasted against C. albicans genome sequence (http://www.candidagenome.org) and S. epidermidis probes with potential match with C. albicans sequences were removed from the array design. Separately, RNA from pure C. albicans cultures were also hybridized to the arrays and cross-hybridizing probes were removed from data analysis.


title: CombiMatrix 90K Petunia inflata array

organism: Petunia integrifolia subsp. inflata

description: 29,163  specific oligos (35-40mer) were designed on Petunia inflata tentative consensus (TC) sequences (JI359155 - JI387099), and by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls, nine bacterial oligonucleotides sequences provided by CombiMatrix were utilized. The 90K TomatArrayTM 1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by CombiMatrix protocols available at the CombiMatrix website (www.combimatrix.com).


title: Agilent-027388 Salmonella typhimurium SL1344

city: Norwich

first: Gaspar

last: Avendano

address: Norwich Research Park, Colney

institute: Institute of Food Research

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

description:
Salmonella Array SL1344

Arrays of this design have barcodes that begin with 16027388 or 2527388.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

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

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


title: AB SOLiD 4 System (Malus x domestica)

status: Public on Feb 24 2012

last: GEO

organism: Malus domestica

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2000 (Malus x domestica)


title: AB SOLiD 4 System (Saccharomyces bayanus x Saccharomyces cerevisiae)

status: Public on Feb 23 2012


title: Illumina Genome Analyzer IIx (Listeria innocua Clip11262)

organism: Listeria innocua Clip11262


title: Illumina Genome Analyzer IIx (Listeria monocytogenes EGD-e)

organism: Listeria monocytogenes EGD-e


title: AB SOLiD 4 System (Saccharomyces arboricola)

organism: Saccharomyces arboricola


title: AB SOLiD 4 System (Saccharomyces bayanus)

organism: Saccharomyces bayanus


title: Custom E. coli K12 8 x 15K format

status: Public on Feb 22 2012

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

institute: Synmikro

organism: Escherichia coli

technology: spotted oligonucleotide

manufacture_protocol: The oligonucleotide microarray is composed of about 15000 of 60 mer oligonucleotides. Each probe matches to one MseI fragment of the E. Coli chromosome with a size between 60 and 1000 bp. The annotation contains the lenght of this MseI fragments and the number of GATC methylation sites on this fragment.


title: RT2 Profiler PCR Array Mouse Apoptosis

status: Public on Feb 20 2012

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

organism: Mus musculus

description: pathway-focused gene expression profiling using real-time PCR

first: D

last: Taylor

first: M

last: Wilkinson

first: J

last: Voyich

first: N

last: Meissner


title: Klebsiella pneumoniae MGH 78578 Nimblegen 9822 array

city: La Jolla

first: Bernhard

last: Palsson

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Dr.

institute: University of California, San Diego

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

description:
Design ID 9822; Order ID 21032; 385K microarray. The .ndf and .ngd files are described below.
native array description file: Kp.ndf
native array description file: Kp.ngd

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


title: AB SOLiD 4 System (Saccharomyces paradoxus)

organism: Saccharomyces paradoxus


title: Agilent-014339 Rat genome CGH 185K microarray

status: Public on Feb 21 2012

city: hachiouji

first: yoshiyuki

last: ishii

address: takakura-cho

country: Japan

institute: Agilent

organism: Rattus norvegicus

description:
AMADID:014339
Data table annotations based on genome build RGSC_v3.1, July 2003.
ID column is feature number of agilent feature extraction.

distribution: commercial


title: CombiMatrix 90K Brassica oligonucleotide array (v1.1)

city: Saskatoon

first: Raju

last: Datla

address: 110 Gymnasium Place

country: Canada

institute: NRC-PBI

organism: Brassica napus

description: probes(35–40 mer oligonucleotide) were in situ synthesized

manufacturer: Plant Biotechnology Institute (Saskatoon, Canada)

manufacture_protocol: 90,564 probes(35–40 mer) were in situ synthesized using the CustomArray Synthesizer (CombiMartix, USA)


title: Illumina Genome Analyzer II (Ipomoea batatas)

status: Public on Feb 17 2012

organism: Ipomoea batatas


title: AB SOLiD System 3.0 (Noccaea caerulescens)

organism: Noccaea caerulescens


title: Exiqon MiRCURY Locked Nucleic Acid array [miRBase 8.2]

city: St Leonards, Sydney

first: Casina

last: Kan

state: NSW

address: RNSH, Pacific Hwy

department: Hormones and Cancer Group

country: Australia

institute: Kolling Institute of Medical Research

organism: Homo sapiens

manufacture_protocol: See manufacturers website


title: harvard_Carpodacusmexicanus_1

city: Moulis

first: Camille

last: Bonneaud

address: Station d'Ecologie Experimentale

institute: Centre National de la Recherche Scientifique (CNRS)

organism: Haemorhous mexicanus

first: Susan

middle: L

last: Balenger

first: Andrew

middle: F

last: Russell

first: Jiangwen

last: Zhang

first: Geoffrey

middle: E

last: Hill

first: Scott

middle: V

last: Edwards

manufacture_protocol:
Microarray construction
We constructed a microarray using cDNA clones from the subtraction suppression hybridisation (SSH) libraries constructed in Wang et al. and enriched in cDNA differentially expressed between MG-infected and control house finches 2-weeks post-infection (4).  The microarray consisted of 1000 unique amplicons and included the 220 clones previously identified as significantlydifferentially expressed between control and infected house finches using a macroarray approach (4), as well as 694 randomly selected clones from the librairies, many of whose expression responses to infection are unknown (4).  The clones were collected from the SSH libraries with a toothpick and grown in 1.3 ml of LB + ampicilin at 37°C overnight.  We isolated the plasmid DNA using a Plasmid & BAC extraction kit (AutoGen) on an AutoGenprep 965.  We amplified 5 µl of the eluted DNA in 10 µl Buffer 10 (Lucigen), 0.8 µl dNTP (100 µM), 8 µl of each primer M13/M13R (10 µM), 0.8 µl (4 U) EconoTaq DNA polymerase (Lucigen) and 56.4 µl of sterile dH2O.  The reaction was run for 35 cycles consisting of a 90s 94°C denaturating step, a 45s 50°C annealing step and a 45s 72°C extension step.  PCR products were purified using a QIAGEN MinElute 96 UF Purification kit and run on a 2% agarose gel.  Amplified inserts were subsequently printed onto the array slides.
We also printed five house finch ‘housekeeping’ genes to help in normalization procedures (Actin related protein 2/3, ATP synthetase, ATPase V1 subunit G1, Basic transcription factor 3, Calmodulin 2; accession numbers: bankit1324533, 1324536, 1324538, 1324542, 1324554).  These genes were generated by amplification of cDNA extracted from house finch spleens (see below), using degenerate primers designed from conserved sequences of humans, mice, chicken and, when available, zebra finches.  We amplified 2 µl of cDNA in 2.5µl Buffer 10 (Lucigen), 2.5 µl dNTP (100 µM), 1 µl of each primer (10 µM), 0.2 µl (2.5U) EconoTaq DNA polymerase (Lucigen) and 15.8 µl of sterile dH2O.  The reaction was run for 35 cycles consisting of a 1 min 94°C denaturating step, a 2 min 60°C annealing step and a 3 min 72°C extension step. PCR products were run on a 2% agarose gel and purified using a QIAGEN MinElute 96 UF Purification kit.  Each gene was amplified twice and while we kept one reaction intact, we ligated and transformed the other into One Shot TOP10 Chemically Competent Escherichia coli using the TOPO Cloning kit (Invitrogen).  Colonies were picked and added to 1.3 ml of LB medium with ampicilin to grow overnight at 37°C.  We then isolated the plasmid DNA using a Plasmid & BAC extraction kit (AutoGen) on an AutoGenprep 965.  We amplified 2 µl of the extracted plasmids in 2.5 µl Buffer 10 (Lucigen), 0.2 µl dNTP (100 µM), 2 µl of each primer M13/M13R (10 µM), 0.2 µl (2.5U) EconoTaq DNA polymerase (Lucigen) and 14.1 µl of sterile dH2O. All PCR products were purified using a QIAGEN MinElute 96 UF Purification kit and run on a 2% agarose gel.  We verified the identity of the purified PCR products by sequencing them on an ABI 377 DNA sequencer (see below).  We printed both the PCR products and the transformed PCR products of the five house finch housekeeping genes onto the array slides.  We quantified purified PCR products on a Nanodrop spectrophotometer.
Additionally, we printed the PCR products from the DNA amplification of 11 E. coli housekeeping genes (arcA, aroE, dnaE, gapA, gnd, icdA, pgm, polB, putin, trpA, trpB) to serve as external spike-ins(5).  DNA was extracted from a few E. coli colonies obtained above using the QIAGEN DNeasy Tissue and we amplified E. coli house keeping genes as described in (6-7).  PCR products were purified, sequenced and quantified as described above.
We printed the clones on poly-L-lysine coated glass slides using an OmniGrid 100 (GeneMachines, BST Scientific).  All clones were printed twice on each grid and each grid was replicated twice on each microarray slide.  After printing, the slides were blocked by rehydration, UV crosslinking at 60 mJ, and dipped in blocking solution (6g Succinic Anhydride, 335 ml 1-Methyl-2-pyrrolidinone, 15 ml Sodium Borate).  Denaturing was subsequently performed by dipping the slides in MiliQ water, and then in 95% Ethanol, and spun dry by centrifugation for 2 min at 1000 rpm.  The desiccated slides were stored at room temperature in a closed container until further use.


title: Mouse Signal Transduction PathwayFinder RT² Profiler™ PCR Array

city: Galveston

first: Dar

last: Heinze

state: Texas

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

technology: RT-PCR

description: PCR assay


title: Mouse Th17 for Autoimmunity & Inflammation RT² Profiler™ PCR Array

description: PCR assay


title: Illumina Genome Analyzer IIx (Strongylocentrotus purpuratus)

status: Public on Feb 16 2012

last: GEO

organism: Strongylocentrotus purpuratus


title: Mouse Extracellular Matrix and Adhesion Molecules RT² Profiler™ PCR Array

description: PCR assay


title: Agilent-021826 UIUC Erwinia 15K.V1.0

status: Public on Feb 18 2012

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

organism: Erwinia amylovora

description: An oligonucleotide microarray was designed at the James Hutton Institute (formerly SCRI), and synthesized by Agilent Technologies, Inc. (Palo Alto, CA). Each slide contains 8 arrays and each array has nearly 15,000 spots, containing our probes in triplicate. The main E. amylovora ATCC 49946 genome (accession NC_013971, Sebaihia et al. 2010) had 3483 target sequences (annotated genes and pseudo-genes), plus a further 483 target genes or simple gene predictions from five sequenced plasmids: plasmids 1 and 2 for the same strain (accessions NC_013972, NC_013973, Sebaihia et al. 2010), pEL60 and pUE30 (accessions NC_005246, NC_005247, Foster et al., 2004), and pEI70 (Spanish strain Erwinia amylovora IVIA1614-2a, unpublished, Lopez and Llop, personal communication). Due to the high similarity between E. amylovora ATCC 49946 plasmid 1 (NC_013972, 2.8kb) and the previously published pEA29 (NC_005706, 2.8kb, McGhee and Jones 2000), the later was not used. Up to five sense orientation candidate probes per target were designed with the Agilent eArray webtool, using temperature matching methodology, a preferred probe melting temperature of 80.0C, no 3' bias, and a target length of 60bp. Any short probes were later extended to 60bp using the Agilent linker. BLASTN (Altschul et al., 1997) and Biopython (Cock et al., 2009) were used to identify potential cross-hybridization in order to rank the candidate probes. Selecting one probe per genome target, and up to five probes per plasmid target, allowed all our probes to be present in triplicate. Using the spare array capacity for multiple plasmid probes aimed to increase the chance of hybridization with plasmid transcripts from other E. amylovora strains.

manufacture_protocol: An oligonucleotide microarray was designed at the James Hutton Institute  (formerly SCRI), and synthesized by Agilent Technologies, Inc. (Palo  Alto, CA). Each slide contains 8 arrays and each array has nearly 15,000  spots, containing our probes in triplicate. The main E. amylovora ATCC  49946 genome (accession NC_013971, Sebaihia et al. 2010) had 3483 target  sequences (annotated genes and pseudo-genes), plus a further 483 target  genes or simple gene predictions from five sequenced plasmids: plasmids  1 and 2 for the same strain (accessions NC_013972, NC_013973, Sebaihia  et al. 2010), pEL60 and pUE30 (accessions NC_005246, NC_005247, Foster  et al., 2004), and pEI70 (Spanish strain Erwinia amylovora IVIA1614-2a,  unpublished, Lopez and Llop, personal communication). Due to the high  similarity between E. amylovora ATCC 49946 plasmid 1 (NC_013972, 2.8kb)  and the previously published pEA29 (NC_005706, 2.8kb, McGhee and Jones  2000), the later was not used. Up to five sense orientation candidate  probes per target were designed with the Agilent eArray webtool, using  temperature matching methodology, a preferred probe melting temperature  of 80.0?C, no 3' bias, and a target length of 60bp. Any short probes  were later extended to 60bp using the Agilent linker. BLASTN (Altschul  et al., 1997) and Biopython (Cock et al., 2009) were used to identify  potential cross-hybridization in order to rank the candidate probes.  Selecting one probe per genome target, and up to five probes per plasmid  target, allowed all our probes to be present in triplicate. Using the  spare array capacity for multiple plasmid probes aimed to increase the  chance of hybridization with plasmid transcripts from other E. amylovora  strains.


title: miRXplore TM Microarray (911)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 6228 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1460 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1460 miRNA sequences covered sequence verified miRNAs of the species human (878) mouse (682) and rat (427) as well as viral miRNAs (141) as deposited in the miRBase sequence database version 14.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: Agilent-027295 Murine herpesvirus 68 array [Feature Number version]

city: Stony Brook

first: Laurie

last: Krug

state: NY

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

organism: Murid gammaherpesvirus 4

description: 4 X 44K array; a total of 11,940 60-mer oligonucleotides with 20-nucleotide spacing were generated based on the MHV68/Murid herpesvirus 4 genomic sequence (NCBI RefSeq NC_001826) to enable triple probe coverage of every nucleotide of both strands of the virus.


title: Agilent-021438 Custom HD-CGH microarray (1x244K)

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

description: Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides mapped to UCSC hg18 human genome (NCBI build 36)


title: Agilent-025537 Murine herpesvirus 68 [Feature Number version]

description: 8 X 15K array; a total of 11,940 60-mer oligonucleotides with 20-nucleotide spacing were generated based on the MHV68/Murid herpesvirus 4 genomic sequence (NCBI RefSeq NC_001826) to enable triple probe coverage of every nucleotide of both strands of the virus.


title: AB SOLiD 4 System (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Illumina Genome Analyzer (Klebsiella pneumoniae)

status: Public on Feb 14 2012

organism: Klebsiella pneumoniae


title: NanoString nCounter mouse miRNA expression platform

city: Bethesda

first: Stefan

middle: Adi

last: Muljo

state: MD

address: 10 Center Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

technology: other

description:
Assay includes probes for the following: 578 mouse miRNAs, 33 viral miRNAs, 6 positive miRNA assay controls, 8 negative miRNA assay controls, 4 mRNA housekeeping controls, and 3 non-mammalian miRNA spike-in probes.
Based on miRBase v.15

middle: A

manufacture_protocol: See manufacturer's website (www.nanostring.com).


title: Human_HG18_Deluxe_Promoter_HX1_HD2.1 tiling array

status: Public on Feb 15 2012

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Oligo coordinates based on genome build HG18.
The array tiles RefSeq genes from -7000 to +3000 relative to the TSS, with 100bp probe spacing.

first: Miao

last: Sun

first: Gary

middle: D

last: Isaacs

first: Nasun

last: Hah

first: Nina

last: Heldring

first: Elizabeth

last: Fogarty

first: William

manufacture_protocol: See Nimblegen website


title: Illumina Genome Analyzer (Escherichia coli K-12)

organism: Escherichia coli K-12


title: [Cotton] Affymetrix Cotton Genome Array

status: Public on Jun 05 2009

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® Cotton Genome Array is a single GeneChip brand array comprised of 23,977 probe sets representing 21,854 cotton transcripts. Sequences used in the design of the array were selected from GenBank®, dbEST, and RefSeq, and were created from the Gossypium hirsutum UniGene database (Build 2, August 2006) and the Gossypium raimondii UniGene database (Build 2, September 2005). These sequences derive from the many contributors from the Cotton Community. Some select sequences were generously made publicly available prior to publication by a group within the Cotton Community specifically to enhance the design of the GeneChip Cotton Genome Array.

The GeneChip® Cotton Genome Array is based on EST sequences from four species of Cotton: Gossypium hirsutum, Gossypium raimondii, Gossypium arboretum, and Gossypium barbadense. The Array was designed in close collaboration with the Cotton Research Community as part of the Affymetrix® GeneChip Consortia Program.


title: NimbleGen Magnetospirillum magneticum str. AMB-1 - 4x72k custom expression array

city: Berkeley

first: Arash

last: Komeili

address: 111 Koshland Hall #3102

department: Plant and Microbial Biology

institute: UC Berkeley

organism: Paramagnetospirillum magneticum AMB-1

description:
Custom 4x72,000 gene expression microarray.
NimbleGen design name 090515_Mmag_SG_exp, NimbleGen design ID 21722. Each 72k expression design contains duplicate coverage of 4350 annotated genes (60mer probes, 7 unique probes per gene). In addition, design contains 7 60mer probes per 22 unannotated ORFs, genomic coordinates of each are listed in SEQ_ID (denoted as genomic region [LDx] _ gene start of region _ gene end of region _ genomic coordinate start _ genomic coordinate end). The microarray design also included tiling of the Magnetosome Island, from genomic coordinates 977403-1097027.  This region was covered by 8038 probes, 50 nt in length.

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/.


title: Applied Biosystems TaqMan Human Stem Cell Pluripotency Array

city: Poitiers

first: ulrich

last: cortes

address: 350 av. Jacques Coeur

institute: CHU Poitiers

description: PCR assay

manufacture_protocol: 90 test genes and 6 endogenous controls according to the I.S.C.I.


title: NimbleGen P. falciparum 3D7 Whole Genome CGH Array [090317_Plasmodium_3D7_WG_CGH]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Plasmodium falciparum

description:
DESIGN_NAME: 090317_Plasmodium_3D7_WG_CGH
DESIGN_ID: 9384

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/


title: SAGE:17:NlaIII:Magnaporthe grisea

status: Public on Feb 12 2012

last: GEO

organism: Pyricularia grisea

technology: SAGE NlaIII

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


title: Illumina Genome Analyzer II (Culex quinquefasciatus)

status: Public on Feb 13 2012

organism: Culex quinquefasciatus


title: Exiqon Caenorhabditis elegans miRNA array [miRCURY LNA Array V.11, miRBase 14.0]

status: Public on Feb 09 2012

city: Stratford

first: Eric

last: Moss

state: NJ

address: 2 Medical Center Dr.

department: Molecular Biology

institute: UMDNJ

organism: Caenorhabditis elegans

description: miRCURY LNA Array Other species Version 11 annotated to miRBase 14.0

middle: G

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Taenia multiceps)

organism: Taenia multiceps


title: Agilent Streptomyces avermitilis 15K [Agilent-020986]

city: shanghai

first: hang

last: wu

address: Huashan Road

country: China

institute: sjtu

organism: Streptomyces avermitilis

description: Arrays of this design have barcodes that begin with 16020986 or 2520986.


title: Agilent-018932 Equine 8X15 Array v1 (Feature Number version)

city: Ithaca

first: Donald

last: Miller

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

institute: Cornell University

organism: Equus caballus

description:
1st Gen Equine Array

Arrays of this design have barcodes that begin with 16018932 or 2518932.
DesignID: 018932

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

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

relation: Alternative to: GPL15217 (Probe Name version)


title: Illumina HiSeq 2000 (Dirofilaria immitis)

organism: Dirofilaria immitis


title: Agilent-034793 Custom Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Bombyx mori

first: Raja

middle: C

last: Mugasimangalam


title: A-UMCU-CE44K-1.0

status: Public on Feb 07 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Frank

last: Holstege

manufacture_protocol: 1. Slides are obtained from a commercial provider (Agilent) and reannotated using blat to obtain the latest gene annotations from ensembl.


title: Agilent-018932 Equine 8X15 Array v1 (Probe Name version)

description:
1st Gen Equine Array

Arrays of this design have barcodes that begin with 16018932 or 2518932.
DesignID: 018932

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Probe Name

relation: Alternative to: GPL15204 (Feature Number version)


title: LC_MRA-1002_miRMouse_18 (miRNA ID version)

status: Public on Feb 10 2012

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

institute: Institute of Military Veterinary Academy of Military Medical Sciences

organism: Mus musculus

description:
Number of unique mature miRNA sequences: 1141
Number of repeats: 3
Number of unique controls: 49

Based on Sanger miRBase release 18.

manufacture_protocol: Arrays are made using µParaflo Microfluidic Chip Technology.


title: PLBIO-DX2010 - Whole Genome 38K expression array

city: Mumbai

first: Geeta

middle: Bhalchandra

last: Godbole

state: Maharashtra

address: Jehangir Merwanji Street, Parel

department: Molecular and Cellular Biology

institute: National Institute for Research in Reproductive Health

organism: Homo sapiens

description: PLBIO-DX2010 - WH/GEX

manufacturer: Biomarker Discovery, Translational Research, Piramal Lifesciences India Limited

manufacture_protocol: A microarray chip with 37,632 transcripts representing the whole human genome were purchased from Operon Biotechnologies (Operon, USA). Every gene was confirmed for function and sequence with the latest RefSeq genome build and represented as a unique 70-mer oligonucleotides sequence. A 40μM concentration of the oligos was achieved by dissolving the oligos with 50% DMSO solution. The MTP plates were vortexed at 150 rpm for 2 hours and spun down at 1200 rpm in a swing out rotor centrifuge. Every gene/oligo was printed with a robotic arrayer – OG100 (Genomic Solutions, Ann Arbor, USA) on aminosilane coated glass slide (ArrayIT, USA). The relative humidity and the temperature were maintained at 45% RH and 23°C. The printing is achieved by contact disposition of 20nL of the oligo suspension onto the glass slide with stealth microarray pins (SMP3) having an uptake capacity of 250 nL. Post printing, the slides were air dried for 6 hours in the printing environment and then cross-linked at 650 mL/sec2 with an UV cross-linker. The slides were then packed and stored under vacuum in the dark at room temperature.


title: 454 GS FLX (Aliivibrio fischeri; environmental samples)

status: Public on Feb 08 2012

organism:
Aliivibrio fischeri
environmental samples


title: Illumina HiSeq 2000 (Bacillus subtilis subsp. subtilis str. 168)


title: NimbleGen-TI272559 Bacteroides fragilis NCTC 9343 385K Expression Array

status: Public on Feb 03 2012

last: Nimblegen Systems

organism: Bacteroides fragilis NCTC 9343

description:
2006-07-27_TI272559_60mer Catalog design for Bacteroides fragilis NCTC 9343 (ATCC 25285) covering NC_003228, NC_006873.Probes selected for 4231/4231 sequences. Median number of probes/sequence is 18 with an average of 18.00.
Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array.
Unused features have been filled with randomly generated probes of comparable GC content.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer technology per manufacturer website .


title: 454 GS FLX (environmental samples)

last: GEO

organism: environmental samples


title: University of Texas UTHSC-H Candida albicans v2.0

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

organism: Candida albicans

manufacture_protocol: 70-mer oligonucleotide set from Qiagen was printed on glass slides.


title: MRA-1031_MiRMammalia_11.0

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

organism:
Lemur catta
Saguinus imperator
Ateles sp.
Lagothrix
Macaca mulatta
Macaca nemestrina
Symphalangus syndactylus
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo abelii
Homo sapiens
Canis lupus familiaris
Sus scrofa
Bos taurus
Ovis aries
Cricetulus griseus
Mus musculus
Rattus norvegicus
Monodelphis domestica
Rhinopithecus bieti

description: catalog number : MRA-1031

manufacture_protocol: Arrays are made based on 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://www.mirbase.org/) 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 HiSeq 2000 (Silene latifolia)

organism: Silene latifolia


title: Caenorhabditis elegans custom miRNA array

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

description: CodeLink® Activated Microarray Slides with a TRIDIA™ NHS Coating. Product Code DN01-0025 – formerly GE Healthcare #300011 (or #256700-00)

first: Martin

middle: J

last: Simard

first: Javier

last: Armisen

manufacture_protocol: Glass slides were arrayed using quadruplicate spots for each of the microRNA probes. Details can be found in: Miska, E. A. et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5, R68 (2004). A .GAL file with spot positions is attached as a raw data file.


title: NimbleGen_mouse(MM9)_Hox plus array [Design_ID:11926]

status: Public on Feb 01 2012

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

description:
DESIGN_ID : 11926

native array description file:100428_PM_MM9_Hox_plus_ChIP.ndf
native array description file:100428_PM_MM9_Hox_plus_ChIP.pos


title: EBT UA_KUL Daphnia magna unique_1.9K microarray

city: Antwerpen

first: Nathalie

last: Dom

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

organism: Daphnia magna

manufacturer: Laboratory for Ecophysiology,biochemistry and toxicology, University of Antwerp, Belgium and Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Belgium

first: Mieke

last: Jansen

first: Tine

last: Vandenbrouck

first: Ronny

last: Blust

first: Luc

last: De Meester

first: Dries

last: Knapen

manufacture_protocol:
This microarray is composed of 3 cDNA libraries which are the result of 3 SSH procedures. One SSH was performed with adult vs juvenile gene pools, one with ecdyson exposed vs control organisms and one with starved vs well fed organisms (Soetaert et al., 2006; 2007). The unique sequences selected via those SSHs were supplemented with additional set of unique gene fragments related selected through 3 other SSHs related to other stress factors (fish, Pasteuria ramosa and carbaryl stress) (Orsine et al., 2011).
In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector specific primers (M13 forward and M13 reverse) and purified by an exosap reaction. In preparation for spotting, cDNA-inserts of the clones were, amplified using adaptor specific primers (nested primers, Clontech), purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at ~150 ng/µl. A Qarray Mini Robot (Genetix) with 16-solid pin-head was used to spot each clone in triplicate onto aminosilane coated glass slides (Generoma microarray slides; Asper Biotech, Estonia).


title: Agilent-015037 Bulyk Human Muscle CRMs 244K v1.0

city: Boston

first: Martha

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics

institute: Brigham and Women's Hospital

description:
The array probes were designed to achieve 25-bp resolution tiling of 100 kb surrounding each of 104 selected human genes, chosen because they were either upregulated over the timecourse of myogenic differentiation, or annotated by Gene Ontology as being a part of the muscle sarcomere. For each of these genes, the array covers -40 kb to +10 kb relative to transcription start and -10 kb to +40 kb relative to transcription stop. Additionally, the array sequence covers: 5 kb around each of 9 negative control regions previously found to be not bound by myogenic TFs; 5 kb around each of 35 potentially regulatory noncoding SNPs, and 5 kb around each of 100 predicted CRMs which are distant (i.e., greater than 50 kb away from the TSS) from annotated muscle-specific or differentially expressed genes. The probe sequences were selected using the microarray design tools available from Gerstein and colleagues (http://tiling.gersteinlab.org/microarray_design.html) to mask repetitive sequences.
catalog number: AMADID # 015037

first: Rachel

middle: P

last: McCord

first: Vicky

last: Zhou

first: Tiffany

last: Yuh

manufacture_protocol: Standard Agilent commercial synthesis protocols


title: CRUK/Melton lab-Human melanoma-71-v2-microRNA expression profiling

first: Yan

last: Xu

address: Crewe Road South

department: MRC

institute: The University of Edinburgh

technology: oligonucleotide beads

manufacture_protocol: The MicroRNA Expression Profiling Assay requires an input of only 100-200 ng of isolated total RNA.The input RNA is polyadenylated and converted to cDNA by standard methods. A single miRNA-specific oligo (MSO) is used to assay each miRNA on the panel. All MSOs are hybridized to the sample in parallel, and a solid-phase primer extension step further increases specificity and reduces noise . Universal amplification of extended products only after this point avoids PCRinduced detection bias. The universal PCR step creates fluorescently labeled products identifiable by their unique MSO sequence. These labeled assay products correspond to, and are in relative abundance to, specific original miRNA in the sample. The address sequence from each MSO is used to hybridize specific miRNA products to specific locations on the BeadArrayTM substrate for readout.


title: WashingtonUniversity_Efimov_Human_Heart_96well_v1

city: St. Louis

first: Christina

middle: Marie

last: Ambrosi

state: MO

address: 1 Brookings Drive

department: Biomedical Engineering

institute: Washington University in St. Louis

description: PCR assay

manufacture_protocol: see manufacturer's website http://docs.appliedbiosystems.com/pebiodocs/00106393.pdf


title: Agilent-020923 ICEclcB13

status: Public on Jun 01 2010

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

organism: Pseudomonas knackmussii

description:
clc element of strain B13

Arrays of this design have barcodes that begin with 16020923 or 2520923.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

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

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


title: [Eh_Eia520620F_Eh] Custom Entamoeba histolytica Eh_Eia520620F_Eh Array

status: Public on Nov 16 2011

city: Shinjuku-ku

first: Gil

middle: Mallari

last: Penuliar

state: Tokyo

address: Toyama 1-23-1

department: Parasitology

institute: National Institute of Infectious Diseases

organism: Entamoeba histolytica

manufacture_protocol: A custom generated Affymetrix platform full genome microarray (E_his-1a520285F). This array has 7,712 unique probe sets representing 9,435 open reading frames (ORFs). Due to the highly repetitive nature of the E. histolytica genome, some of the probe sets are predicted to cross-hybridize with other sequences. Probe sets that represent a single gene are labeled as (_at). Probe sets in which at least one probe may cross-hybridize with another gene(s) are labeled as (_x_at). In situations where all the probe sets for a given gene cross-hybridize with another gene(s), the probe sets are labeled as (_s_at) and additional genes that cross-hybridize with these probe sets are listed in Supplementary Table 2. This array also contains probes for intergenic non-coding regions, however, these are not included in this submission.


title: FGAS/USDA/ACPFG-Wheat-17K-v1.0

first: Jesse

middle: D.

last: Munkvold

address: 240 Emerson

department: Plant Breeding and Genetics

organism: Triticum aestivum

manufacture_protocol: The Triticum aestivum 17K 70mer oligo microarray was developed with the international collaboration of three partners, the Genome Canada/Genome Prairie/Genome Quebec program Functional Genomics of Abiotic Stress (FGAS), the USDA-ARS, Genomics and Gene Discovery Research Unit, Albany California, and the Australian Centre Plant Functional Genomics.   The source sequences are primarily derived from the NSF wheat EST and FGAS programs. The 70bp oligonucleotide probes were synthesized by Qiagen (Valencia, CA) and spotted on Corning UltraGAPS II slides by Microarrays Inc. (www.microarrays.com). The design of the 70mer oligonucleotides was based on an internal project EST assembly that used all available EST data at the time, which means that each contig contains information from many different ESTs.


title: SHEZ

status: Public on Sep 14 2007

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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


title: SHEY


title: A-UMCU-C44K-1.0

first: Patrick

last: Kemmeren

organism: Canis lupus familiaris

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Frank

last: Holstege


title: SHEX


title: Cornell Mparatuberculosis_K10 4.5K Genome Array

status: Public on Oct 22 2009

city: Brookings

first: Joy

last: Scaria

state: SD

department: Veterinary and Biomedical Sciences

institute: South Dakota State University

organism: Mycobacterium avium subsp. paratuberculosis K-10

first: Jenn-Wei

last: Chen

first: Yung-Fu

last: Chang

manufacture_protocol: This array consists of 60mers representing each CDS in Mycobacterium avium subspecies paratuberculosis K10 genome. Probes were designed using Agilent technologies E-array (http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx) expression algorithm. One probe was designed for each CDS and each probe was printed in triplicate using Agilent Sureprint technology.


title: febit Homo sapiens miRBase 15.0

status: Public on Feb 02 2012

city: Erlangen

first: Michael

middle: Georg

last: Schrauder

address: Universitätsstrasse 21-23

department: Gynecology

institute: University Hospital Erlangen

manufacture_protocol: MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.  Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.  MPEA: On-Chip Labeling for Highest Sensitivity  Enzymatic labeling assay requires minimal sample amount  In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.  MPEA benefits  * Higher sensitivity and specificity  * miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias  * High discriminatory power  * Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)  * Easy to use protocol for Geniom RT Analyzer    The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.  The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.  Details provided at www.febit.com


title: Print_1225

status: Public on Jun 20 2008

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine


title: Agilent-016271 rainbow trout 37K oligo array [Feature number version]

status: Public on Feb 27 2009

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

organism: Oncorhynchus mykiss

description: Custom Microarrays

first: Caird

last: Caird Rexroad III

first: Jianbo

last: Yao

manufacture_protocol: A total of 37,394 unique rainbow trout transcript-specific oligonucleotide probes were used to construct a high-density rainbow trout microarrays. The probes, 60-mer long, were designed based on sequences from Rainbow Trout Gene Index TCs (Release 6.0, June 19, 2006, http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_ann.pl?gudb=r_trout). Probes were checked for possible non-specific mRNA cross-hybridization problems by comparing all individual probes with all rainbow trout transcriptome sequences. A probe design file was created to print the probes randomly on an Agilent 4 X 44 design format that contains 1417 Agilent control spots for quality control. The microarrays were synthesized in situ using the non-contact inkjet technology.


title: cph

status: Public on Aug 09 2007

organism: Francisella tularensis


title: NimbleGen_101221_P. involutus ATCC200175_TJ_EXP_HX12 [DesignID : 546871]

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

department: MEMEG

country: Sweden

institute: Lund University

organism: Paxillus involutus ATCC 200175

description:
NimbleGen design name 101221_ATTCC200175_TJ_EXP_HX12
NimbleGen design OID 33038
NimbleGen DESIGN_ID: 546871
A expression design for 12,214 gene models from the ectomycorrhizal fungus Paxillus involutus ATCC 200175 with approx. 10 tiled 60-mer probes per gene.

A web database containing sequences and annotation for the 12,214 gene models here used (mbio-serv2.mbioekol.lu.se/Paxillus/Hybrid/)

native array description file: 101221_ATCC200175_TJ_EXP.ndf
native array description file: 101221_ATCC200175_TJ_EXP.ngd

manufacture_protocol: High-density 12-plex DNA arrays (HD2: 12x135K Format) prepared with Maskless Array Synthesizer (MAS) technology (www.nimblegen.com).


title: ScoKao_01-11-09

last: Stanford Microarray Database

organism: Streptomyces coelicolor


title: Agilent Yeast Whole Genome ChIP-on-chip Microarray

status: Public on Mar 10 2006

first: Stephen

last: Bell

address: 77 Massachusetts Ave

institute: MIT

organism: Saccharomyces cerevisiae

description: Agilent's Yeast Whole Genome ChIP-on-chip Microarray Set is specifically designed for use with the method of location analysis of DNA binding proteins in S. Cerevisiae. ChIP-on-chip pairs chromatin immunoprecipitation (ChIP) with Agilent DNA microarrays. Each microarray is printed on a single slide and contains optimized and validated probes that cover over 85% of the non-repetitive part of the yeast whole genome (12 MB).

manufacture_protocol: see manufacturer's website


title: [Vharveyis520694F] US Naval Research Laboratory V campbellii BAA-1116 whole genome microarray

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

description: Affymetrix DNA microarray (Vharveyi520694F) that targets 4831 total CDS from the fully assembled and annotated V. harveyi BAA-1116 genome (Naval Research Laboratory sequencing effort GenBank CP001223-5)

manufacture_protocol: see manufacturer's web site


title: Eurogentec S. pombe IGR+ORF array (J120E)

status: Public on Jan 12 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

first: K

first: A

last: Wright

first: D

last: Talibi

first: S

last: Hass

manufacture_protocol:
Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: SHFE

organism: Homo sapiens


title: NimbleGen C_elegans_WS170_Tiling_Iso_HX1 tiling design

status: Public on Jul 25 2008

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Caenorhabditis elegans

description: Tiling array using NimbleGen platform (DesignID=6112). WormBase release WS170. Complete tiling of pseudo-chromosomes; no filtering; isothermal (target tm=76); mean probe length=54 (range=50 to 75); mean distance between probes=-6 (range=-18 to 1111); all probes on forward strand.

first: Barbara

last: Meyer

first: Steven


title: VIMSS Desulfovibrio vulgaris Hildenborough 7K v2.0

status: Public on May 30 2007

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

first: Marcin

last: Joachimiak

manufacture_protocol: Thompson, D., Beliaev, A., Giometti, C., Tollaksen, S.,Khare, T., Lies, D., Nealson, K., Lim, H., Yates, J., Brandt, C. Tiedje, J., and Zhou, J. 2002. Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress. Appl. Environ. Microbiol. 68:881-892.


title: MSU2_06-00

status: Public on Dec 03 2005

organism: Arabidopsis thaliana

manufacturer: Jeremy,,Gollub; CCSR 2255, Stanford, California  94305; 650-736-0075; jgollub@genome.stanford.edu


title: SHCX

status: Public on Dec 30 2005


title: SHDI

status: Public on Jan 06 2006


title: SHDT

status: Public on Jan 07 2006


title: SHEN

status: Public on Jan 21 2006


title: SHBQ

status: Public on Nov 03 2005


title: SHCB

status: Public on Nov 23 2005


title: SHBT

status: Public on Nov 04 2005


title: SHAZ

status: Public on Nov 24 2005


title: SHBH

status: Public on Oct 13 2005


title: Illumina Human660W-Quad v1.0 BeadChip

status: Public on Jul 27 2009

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: See manufacturer's website