title: NimbleGen_Xylella fastidiosa 9a5c_4x72K array

status: Public on Aug 31 2010

city: Cordeiropolis

first: Alessandra

middle: Alves

last: De Souza

state: Sao Paulo

address: Rod Anhanguera KM 158

department: Centro de Citricultura Sylvio Moreira

country: Brazil

institute: Instituto Agronomico de Campinas

organism: Xylella fastidiosa 9a5c

technology: in situ oligonucleotide

description:
Design Name: TI160492
probe size: 60mer
Catalog design for Xylella fastidiosa 9a5c (Taxonomy Id: 160492) covering NC_002488 (Xylella fastidiosa 9a5c, complete genome), NC_002489 (Xylella fastidiosa 9a5c plasmid pXF1.3, complete sequence), NC_002490 (Xylella fastidiosa 9a5c plasmid pXF51, complete sequence). Probes selected for 2832/2832 sequences. Median number of probes/sequence is 13 with an average of 13.00. 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.
The design (.ndf) file and description (.ngd) file are linked below as Supplementary files.

distribution: commercial

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


title: WUSTL Brugia malayi v.1 (condensed version)

status: Public on Aug 30 2010

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

country: USA

institute: NIH/NIAID

organism: Brugia malayi

technology: spotted oligonucleotide

description:
B. malayi clusters for arrays were selected from 8392 clusters generated and posted in Nembase http://www.nematodes.org/
These clusters were derived from > 20 cDNA libraries that represent the major B. malayi life cycle stages.  They represent approximately ~40% of the total number of predicted genes for B. malayi.
Keywords = brugia malayi nematode worm parasite filaria filariasis
This platform is a condensed version of accession number GPL1483.

distribution: non-commercial

manufacture_protocol: Clusters with multiple ESTs, predicted homology by BLAST, and sequence permitting design of a unique 65-mer oligonucleotides were chosen for inclusion on the array.  Oligos were synthesized from the consensus sequence of selected clusters (n=3569) by standard methods by Illumina (San Diego, CA).   The oligonucleotides (50nM in 3x SSC with 0.75M betaine) were printed in duplicate on MWG Epoxy slides (MWG Biotech Inc, High point, NC) by a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/ ).


title: UMN/Agilent Candida albicans 165K tiling array

city: Boston

first: Amnon

last: Koren

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

organism: Candida albicans

description:
019096_D_20080121
4x44K tiling array for chromosomes 2,3,5,7
Genome version: Assembly 21; 25-Nov-2008; http://www.candidagenome.org/download/sequence/Assembly21/current/
60-mer oligonucleotides.

distribution: custom-commercial

manufacture_protocol: See manufacturer's website.


title: OSU-CCC ucRNA chip version 4

status: Public on Aug 24 2010

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

organism: Homo sapiens

description:
OSU-CCC ucRNA chip version 4
ucRNA sequences might be found at the weblink specified below

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The ucRNA microarray probe set is based on 40mer oligonucleotides.   Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Agilent Mouse 44k Sense-Antisense Transcript Microarray

status: Public on Aug 26 2010

city: Tsukuba

first: Yutaka

last: Watanabe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center (BRC)

country: Japan

institute: RIKEN Tsukuba Institute

organism: Mus musculus

first: Koji

last: Numata

first: Shinya

last: Murata

first: Yuko

last: Osada

first: Rintaro

last: Saito

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazufumi

first: Hidemasa

last: Kato

first: Kuniya

last: Abe

first: Hidenori

last: Kiyosawa

manufacture_protocol: See manufacturer's web site


title: Agilent Mouse 244k CpG-island-associated SAT promoter array


title: UMN/Agilent Candida albicans 200K tiling array

description:
Candida016017_D_20070221
2x105K tiling array for chromosomes R-7
Genome version: Assembly 19; 24-Aug-2009; http://www.candidagenome.org/download/sequence/
60-mer oligonucleotides.


title: Custom Arabidopsis 22K 60-mer oligo array

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

organism: Arabidopsis thaliana

description: target transcript description (Aug 2001 annotation)

manufacture_protocol: Agilent long oligonucleotide array printing protocol (Apr 2002).


title: JCVI PFGRC Vibrio parahaemolyticus 21K v2 array designed primarily based on strain N16961

status: Public on Aug 22 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Vibrio parahaemolyticus

description: This set includes 9232 oligonucleotides, has 21168 spots distributed in 48 blocks.

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


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS8232

organism: Streptococcus pyogenes

description: This set includes 9363 oligonucleotides, has 21168 spots distributed in 48 blocks.

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


title: JCVI PFGRC Vibrio parahaemolyticus 21K v2 array designed primarily based on strain RIMD_2210633


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS10270


title: JCVI PFGRC Vibrio parahaemolyticus 21K v2 array designed primarily based on strain KXV237


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS10394


title: Agilent Trisomy Msp1 Methylation h2b

status: Public on Aug 27 2010

city: Pittsburgh

first: Tianjiao

last: Chu

state: PA

address: 204 Craft Ave

institute: Magee Womens Research Institute

description: based on genome build 36 (hg18)

manufacture_protocol:
1. All MspI enzyme recognition site (CCGG) located on chromosomes 13, 18, and 21 of the human genome were identified
2. 57 bases sequences adjacent to the MspI sites were retrieved.
3. Overlap sequencing were removed.
4. In total, 215060 sequences were identified, and uploaded to the contributor's (David Peters) account at the Agilent E-Array web: https://earray.chem.agilent.com/earray/
5. E-Array design tool for GGH arrays was used to create a custom CGH E-Array template.
6. Custom E-Array ordered from Agilent.


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS9429


title: Lactobacillus reuteri 6475 2.3K v1.0

status: Public on Aug 29 2010

city: Houston

first: Delphine

last: Saulnier

state: TX

address: Feigin Center, Suite 830, 1102 Bates Avenue

department: Pathology

institute: Baylor College of Medicine

organism: Limosilactobacillus reuteri

description:
Lactobacillus reuteri ATCC PTA 6475
Corning UltraGAPS

manufacturer: Michigan State University Research Technology Support Facility

first: Jeoff

last: landgraf

first: Robert

last: Britton

first: James

last: Versalovic

manufacture_protocol:
Oligos arrayed in low volume Greiner 384 well plates in 3X SSC at a final concentration of 30uM.
Arrays printed using a GeneMachines Omnigrid 100 robot with TeleChem Chipmaker 3 pins.
Printing conditions: room temperature, 60% humidity.
Oligo plates sealed with Erie Scientific Titer-Tops, placed in a zip-loc bag and stored frozen at -20C.


title: DeRisi_8Mer_1457_v1

city: San Francisco

first: Polly

last: Fordyce

state: CA

address: 1700 4th St, Byers Hall Room 403

institute: UCSF

organism: synthetic construct

description: Cy5-labeled dsDNA was diluted to a final concentration of 1.25 μM in 3× SSC with 0.125% polyethylene glycol (PEG) (Fluka) and 12.5 mg/mL d-(+)-trehalose dihydrate (Fluka) (for enhanced subsequent solubility) and printed onto custom 2″ × 3″ ThermoFisher Scientific SuperChip Epoxysilane slides (ThermoFisher Scientific) using a DeRisi lab custom microarrayer with 75 um silicon tips.  Arrays were printed using 12 tips in a single row with a 65 spot sector width, 320 um column spacing, and 900 um row spacing.

middle: M

first: Doron

last: Gerber

first: Danh

last: Tran

first: Jiashun

last: Zheng

first: Hao

last: Li

first: Joseph

middle: L

last: DeRisi

first: Stephen

middle: R

last: Quake

manufacture_protocol: Sequences were hybridized to a single Cy5-labeled oligonucleotide (5'-Cy5-GTCATACCGCCGGA-3') (IDT) and extended using Klenow fragment (exo-) (New England Biolabs) to produce Cy5-labeled dsDNA. Final reaction conditions were 100 uM each dNTP, 5 uM Cy5-labeled oligonucleotide, 5 uM library oligonucleotide, and 2 units of Klenow fragment (exo-) in 1x NE Buffer 2.  Reactions were initally prepared without Klenow fragment (exo-), denatured at 94C for 3 min, and cooled to 37C over 45 min.  Following addition of Klenow fragment (exo-), reactions were incubated at 37C for 1 hour to allow complete extension, following by heat inactivation of the enzyme at 72C for 20 minutes and slow cooling (45 min) back to 10C.


title: NimbleGen human chromosome 7 12x125K

status: Public on Aug 28 2010

first: Pawel

last: Stankiewicz

address: One Baylor Plaza

department: Molecular Human Genetics

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


title: Illumina Genome Analyzer (gut metagenome; Hirudo verbana)

last: GEO

organism:
Hirudo verbana
gut metagenome

technology: high-throughput sequencing

distribution: virtual


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS10750


title: Illumina Genome Analyzer II (Plasmodium falciparum 3D7)

organism: Plasmodium falciparum 3D7


title: Custom NimbleGen human microRNA promoter array [071121_HG18_ncRNA]

middle: Leo

last: Wiemels

address: 1450 3rd Street, MC 0520

description:
HG18
non-coding RNA design covering regions of miRNA, piRNA and snoRNA at the 50 bp spacing; and the manual regions of encode HG18 at 100bp; plus 12 housekeeping genes. Each ncRNA tiled region spans approximately 15Kb upstream and 10Kb downstream of transcriptional start site.


title: Agilent-024129 Dano rerio 44K

status: Public on Feb 07 2011

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

organism: Danio rerio

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


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain SF370

last: JCVI


title: UTHSC/Kotb Streptococcus pyogenes 2.3K v2

city: St Lucia

first: Peter

middle: G

last: Maamary

address: Cooper Road

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: University of Queensland

manufacturer: Molecular Resource Center, University of Tennessee Health Science Center

manufacture_protocol: This oligonucleotide microarray displays probes representing M1 core ORFeome in addition to ORFs representing various M1, M3, M18, and S. dysgalactiae prophages. The microarray was an expansion of one described previously (GEO Platform GPL7661). Oligomers (70mers) were printed in the Molecular Resource Center, UTHSC by the use of MicroGrid II (Genomic Solutions). Additional 70mers, representing M1T1-specific prophages and prophage 3396 of S. dysgalactiae, were designed in batch according to the same design criteria applied for the other oligomers (Oligo Wiz 2.0, URL: http://www.cbs.dtu.dk/services/OligoWiz) and obtained from Integrated DNA Technologies.


title: JCVI PFGRC Vibrio parahaemolyticus 21K v2 array designed primarily based on strain AQ3810


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain SSI


title: febit mus musculus miRBase V14

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

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: UniMuenster-HomoSapiens-30K-Promoter_v1

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

description: Human putative promoter sequences of all known genes and sca/miRNA genes were downloaded from UCSC Golden Path Database based on NCBI Build 35. The putative promoter sequences were defined as 2,000 bases upstream and 1,000 bases downstream from transcription start site. Sequences were repeat-masked. Probes were designed from the sense strand of the non-repeat-masked portions of the promoter regions, with these probe restrictions: 1) Length: 46 – 55 bases 2) Tm: 69 – 79 °C 3) Creatable by NimbleGen in 148-rounds of A, C, G, T. 4) Probe must not contain simple repeats. 5) Probe must not have tendency to form secondary structure. A second set of miRNA probes was created with a slightly looser length restriction of 40 – 60 bases, to be used for hard-to-cover miRNAs. The number of probes was reduced by choosing the closest probe to every position in the promoter that was a multiple of 25, thus spacing the probes roughly 25 bases apart. Probe specificity was screened by aligning them to the human genome using Blat. Probes that had imperfect matches in the genome of 30 bases or more were thrown out, as were probes that had more than 2 exact matches. Up to 2 upstream probes and 1 downstream probe were selected for each promoter region, with an attempt made at sharing probes among overlapping promoter regions.  Priority was given to probes that contained the degenerate sequence RCG or CGY, and that were found within 1000 bases upstream and 500 bases downstream of the start of transcription. Genes with known functions were prioritized for oligo synthesis. Most genes have three representative oligos. After addition of controls, the final array contained the following numbers of spots: 288 blank spots, 366 spotting buffer spots, 192 GFP spots, 176 Salmonella spots and 30178 regular spots.

manufacture_protocol: Oligonucleotides were synthesized with 5´ aminolinker by Operon (Cologne, Germany) and spotted onto Nexterion slides.


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS6180

first: PFGRC


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS2096


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS315


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain 71-724


title: JCVI PFGRC Streptococcus pyogenes 21K v2 array designed primarily based on strain MGAS5005


title: Synovial protein array 0.2K v1.0

status: Public on Aug 21 2010

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

organism:
Homo sapiens
Mus musculus

technology: spotted peptide or protein

manufacturer: Robinson Lab, Stanford University School of Medicine


title: SMD Print_848

status: Public on Aug 20 2010

first: Hongjuan

last: Zhao

address: 300 Pasteur Drive

department: Urology, Edwards Building R116

technology: spotted DNA/cDNA

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: SMD Print_1087


title: SMD Print_771


title: SMD Print_999


title: SMD Print_940


title: Pseudomonas putida KT2440 Mycroarrays

city: College Station

first: Yunho

last: Lee

address: 1501 Harvey Road

department: Chemical engineering

institute: Texas A&M

organism: Pseudomonas putida

description:
The method is described at http://www.mycroarray.com/technology/synthesis.html.
Probe design software searches for specific probes at the genomic level. The probe candidate is compared to all other expressed sequences from the same organism and the thermodynamic parameters (free energy and melting temperature) are computed for all possible hybridizations between the probe and perfect or non-perfect complementary sequences. If all of these values fall below a predetermined threshold, the probe is considered to be specific to its target. Probes are also selected to be unable to fold into stable secondary structures that may interfere with hybridization. Any probes with low sequence complexity or long stretches of the same base are rejected..

first: Jinki

last: Yeom

first: Jisun

last: Kim

first: Jaejoon

last: Jung

first: CheOk

last: Jeon

first: Woojun

last: Park

manufacture_protocol:
See manufacturer's web site
(http://www.mycroarray.com/technology/synthesis.html)


title: TaqMan® Rodent miRNA A+B Cards Set v2.0

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

country: Canada

institute: health canada

organism:
Mus musculus
Rattus norvegicus

technology: RT-PCR

description: The TaqMan® Rodent MicroRNA Array Set v2.0 is a two card set containing a total of 364 TaqMan® MicroRNA Assays per card. The set enables accurate quantitation of 518 and 303 unique microRNAs for mouse and rat respectively in as little as 5 hours. Included on each array is three TaqMan® MicroRNA Assay endogenous controls for each species to aid in data normalization and one TaqMan® MicroRNA Assay not related to human as a negative control. Details on the included assays is available in the Target List file. Purchase of the Megaplex RT Primers, Rodent Pool Set is required to run this array set. An additional preamplification step is enabled by Megaplex PreAmp Primers, Rodent Pool Set for situations where sensitivity is of the utmost importance and/or sample is limiting.


title: Nimblegen Escherichia coli K12 (071112_Ecoli_K12)

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

organism: Escherichia coli str. K-12 substr. MG1655

manufacture_protocol: NimbleGen Protocol.


title: Agilent-022980 Human Gdi1-dupl-jvdw 45k array

status: Public on Aug 17 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
Arrays of this design have barcodes that begin with 16022980 or 2522980.
Orientation: Features are 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.

A custom designed 4x44k Xq28 region-specific oligo-array (Agilent Technologies) that covers the repeat-masked region 152.70 Mb to 153.65 Mb at tiling resolution.

Platform data table annotations based on genome build NCBI 36.1 (Hg18).

first: Joke

last: Vandewalle

first: Guy

last: Froyen

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


title: GeneFilter Human Microarray (GF202)

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center


title: V6.4 BAC-Emulation Oligonucleotide Array

first: zhishuo

last: ou

department: Molecular and Human Genetics

institute: Baylor College of medicine

manufacture_protocol:
See manufacturer's web site
The BAC emulated Version 6.4 OLIGO array was comprised of approximately 43,700 oligonucleotides representing 1400 BAC clones, covering ~150 genomic disorders, all 41 subtelomeric regions up to 12 Mb and 43 pericentromeric regions with backbone coverage of every chromosome at the 650-band level of cytogenetic resolution (http://www.bcm.edu/geneticlabs/cma/tables.html). This targeted OLIGO array corresponds to genomic regions covered by the V6 BAC arrays and was manufactured in a 4 x 44K format with an average of 28-30 oligos per region previously covered by a single BAC clone.


title: SMD Print_877


title: Illumina Genome Analyzer (Escherichia coli; Saccharomyces cerevisiae)

status: Public on Aug 19 2010

last: GEO

organism:
Escherichia coli
Saccharomyces cerevisiae


title: SMD Print_997


title: V6.1 BAC-Emulation Oligonucleotide Array

manufacture_protocol:
See manufacturer's web site
The BAC emulated Version 6.1 OLIGO array was comprised of approximately 42,460 oligonucleotides representing 1400 BAC clones, covering ~150 genomic disorders, all 41 subtelomeric regions up to 12 Mb and 43 pericentromeric regions with backbone coverage of every chromosome at the 650-band level of cytogenetic resolution (http://www.bcm.edu/geneticlabs/cma/tables.html). The 42.46K oligonucleotides (oligos) were selected from initial testing of 105,000 oligos derived from the Agilent eArray library with strict selection criteria and removal of repetitive sequences to ensure optimal performance with greater dynamic range. This targeted 42.46 K OLIGO array (V6 OLIGO) corresponds to genomic regions covered by the V6 BAC arrays and was manufactured in a 4 x 44K format with an average of 28-30 oligos per region previously covered by a single BAC clone.


title: SMD Print_932


title: SMD Print_1009


title: Applied Biosystems Taqman miRNA Expression Assays A and B

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description: Taqman Array A and B for miRNA from Applied Biosystems

manufacture_protocol: see manufacturer's website


title: V6.3 BAC-Emulation Oligonucleotide Array

manufacture_protocol:
See manufacturer's web site
The BAC emulated Version 6.3 OLIGO array was comprised of approximately 43,580 oligonucleotides representing 1400 BAC clones, covering ~150 genomic disorders, all 41 subtelomeric regions up to 12 Mb and 43 pericentromeric regions with backbone coverage of every chromosome at the 650-band level of cytogenetic resolution (http://www.bcm.edu/geneticlabs/cma/tables.html). This targeted OLIGO array corresponds to genomic regions covered by the V6 BAC arrays and was manufactured in a 4 x 44K format with an average of 28-30 oligos per region previously covered by a single BAC clone.


title: BAC V5 array

manufacture_protocol: Version 5 BAC array contained 853 BAC/PAC clones designed to cover genomic regions of 75 known genomic disorders, all 41 subtelomeric regions, and 43 pericentromeric regions.


title: Agilent-023456 Custom BCM-Beaudet Human 180K V8cleaned aCGH Array

first: April

middle: Burant

last: Hall

description:
array Comparative Genomic Hybridization (arrayCGH)
180K array with 30kb backbone coverage and exon by exon coverage for 1714 genes reported to be associated with or cause disease
v8 chip after cleaning
Arrays of this design have barcodes that begin with 16023456 or 2523456.

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.


title: SMD Print_1059

last: Zhao


title: MdoFruit_UCDavis_ADand_052606_4302_12k

city: Davis

first: Abhaya

last: Dandekar

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

organism: Malus domestica

description: In a few instances, targets of oligo probes lack a GenBank accession. The sequences of these and all probes on the array are included in the platform table.

manufacture_protocol:
Oligonucleotide probes for the entire array were designed in one step using an algorithm provided by CombiMatrix. Probes 35-40 nt in length with predicted Tms within a 5ºC window were randomly distributed across the surface of the array in a layout file. This was used to direct synthesis of oligonucleotides at each site on the array. A total of 12,395 probes were synthesized, of which 474 were control probes and 11,921 probes represented apple genes.
Using CustomArray 12k (oligonucleotide), probes were synthesized directly on the chip surface, composed of a proprietary porous reaction layer. 12k arrays consist of 12,000 user definable oligonucleotide features, 35-40 nt optimum. Under each probe, a semiconductor electrode used electrochemical detritylation to control sequence synthesis at that spot without a physical mask as in lithographic synthesis. The process yields a 44 micron feature with 1.5 picomole sensitivity. The arrays were designed for one-color biotinilated hybridization experiments.


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Brainarray CustomCDF, HGU133Plus2_Hs_UG_Version 11.cdf)

status: Public on Aug 16 2010

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

description: Refer to http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/ug.download/HGU133Plus2_Hs_UG_11.0.1.zip

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

manufacture_protocol: see the Affymetrix website


title: Stanford Microarray Functional Genomics Homo sapiens 34.6K

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna


title: BAC V5.1 array

manufacture_protocol: Version 5.1 BAC array contained 853 BAC/PAC clones designed to cover genomic regions of 75 known genomic disorders, all 41 subtelomeric regions, and 43 pericentromeric regions.


title: Agilent-024504 Yersinia_CGH_20090707

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

organism: Yersinia

description: Yersinia species CGH array. Arrays of this design have barcodes that begin with 16024504 or 2524504.. 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..


title: NimbleGen Leishmania infantum JPCM5 8k Expression Array

status: Public on Aug 15 2010

city: Seattle

first: Dhileep

last: Sivam

state: WA

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

organism: Leishmania infantum JPCM5

description:
60mer probes were designed to known coding regions of Leishmania infantum strain JPCM5.  Approximately 10 probes were designed to each protein coding gene, 3 probes to each RNA genes and the remaining probes were evenly distributed through the genome. Probe sequences can be found in the ndf file.

NimbleGen array description files are linked below as supplementary files:
2006-12-20_PM_LINF_expr.ndf
2006-12-20_PM_LINF_expr.ngd

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


title: Agilent-023215 lac

city: Shanghai

first: xk

last: teng

state: Shanghai

address: 151 LiBing R.d

department: technical support

country: China

institute: ShanghaiBio

organism: Lacticaseibacillus casei str. Zhang

description: This array contains 60-mer probes that are designed for L. casei strain Zhang. The sequence of this organism in present in public databases, Acc.No.CP001084.

first: yi

last: zhang

first: xiaoyan

last: mao

manufacture_protocol: available at www.agilent.com


title: Illumina Genome Analyzer (Solanum pennellii)

status: Public on Aug 11 2010

organism: Solanum pennellii


title: 081118_Sims_GIS_multi_Burkh_cgh

status: Public on Aug 14 2010

city: SINGAPORE

first: BERNICE

middle: MENGQI

last: SIM

state: SINGAPORE

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

department: INFECTIOUS DISEASES 2

country: Singapore

institute: GENOME INSTITUTE OF SINGAPORE

organism: Burkholderiales

description:
Using the NimbleGen proprietary photolithography Maskless Array Synthesizer (MAS) technology in situ oligo-synthesis, we fabricated a multi-species pan genome array that has 388943 probes, of which 366064 are data probes, 2074 control probes and 20,000 probes for backgroun estimation and correction. The make-up of these data probes are 55% (of which 60% from Bp K96243) for all sequenced Bp strains, 34% designed for all sequenced Bt strains (of which 90% from Bt E264) and finally 11% designed for Bc strain J2315. The pan genome array has an average melting temperature of 83degC and has a range from 65.4degC to 97.3degC. The average probe length is 50bp, with an average spacing of 60 to 62 bp after removing all repetition and homo-polymer runs.
native array description file: 081118_Sims_GIS_multi_Burkh_cgh.ndf
native array description file: 081118_Sims_GIS_multi_Burkh_cgh.pos


title: VTT Technical Research Centre of Finland Trichoderma reesei intergenic 170K tiling version1

status: Public on Aug 13 2010

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

organism: Trichoderma reesei

middle: I

manufacture_protocol: Standard Nimblegen protocol


title: Illumina Genome Analyzer II (Schizophyllum commune)

status: Public on Aug 12 2010

organism: Schizophyllum commune


title: Illumina Genome Analyzer (Solanum lycopersicum x Solanum pennellii)


title: Illumina Genome Analyzer II (Candida glabrata)

organism: Nakaseomyces glabratus


title: Illumina Genome Analyzer II (Phytophthora phaseoli)

status: Public on Aug 06 2010

organism: Phytophthora phaseoli


title: Bead-based microRNA platform 0.435K

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

manufacture_protocol: Luminex xMap beads were coupled with animo-labeled antisense oligonucleotides to microRNAs, synthesized by IDT Inc.


title: Illumina Genome Analyzer II (Saccharomyces bayanus)

organism: Saccharomyces bayanus


title: Maqbool et al Drosophila 14K DGRC2 oligo platform

city: Bloomington

first: Brian

middle: R.

last: Calvi

state: IN

department: Biology

institute: Indiana University

organism: Drosophila melanogaster

manufacturer: Drosophila Genomics Resources Center, Center for Genomics and Bioinformatics, Indiana University,  Bloomington, Indiana 47405

manufacture_protocol:
Cherbas L., K. Bogart, Y. Zou, P. Cherbas, and J. Andrews 2006.
DGRC-2: Spotted oligonucleotide transcriptome microarrays for the Drosophila community.
CGB Technical Report 2006-01
doi: 10.2506/cgbtr-200601


title: Illumina Genome Analyzer II (Saccharomyces kudriavzevii)

organism: Saccharomyces kudriavzevii


title: University of Chicago Pan custom tRNA arrays

status: Public on Aug 01 2010

city: Chicago

first: John

middle: Michael

last: Zaborske

state: IL

address: 929 E 57th St

department: Biochemistry and Molecular Biology

institute: University of Chicago

organism: Saccharomyces cerevisiae

manufacture_protocol: See manufacturer website.


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain Mu50 (all spots)

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

institute: Austin Health

organism: Staphylococcus aureus

manufacture_protocol: 6QSA, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Agilent-Mouse-Array-018016_D_20071031

status: Public on Aug 05 2010

city: Chapel Hill

first: Susan

middle: C

last: Wu

address: 32-026 Lineberger Comprehensive Cancer Center

department: Biochemistry

institute: UNC Chapel Hill

organism: Mus musculus

description: Three unique 60nt probes were designed for each entry in the Fantom3 database and were synthesized along with lineage marker control probes on a 2x105K format array.

first: Eric

last: Kallin

first: Yi

last: Zhang

manufacture_protocol: Agilent


title: UGAmamlab_Roseoarray_12k_v2

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

organism:
Sulfitobacter sp. EE-36
Roseovarius nubinhibens ISM
Ruegeria pomeroyi DSS-3
Pseudooceanicola batsensis HTCC2597
Jannaschia sp. CCS1
Ruegeria sp. TM1040
Yoonia vestfoldensis SKA53
Oceanicola granulosus HTCC2516
Roseobacter sp. MED193
Roseovarius sp. 217
Sulfitobacter sp. NAS-14.1
Sagittula stellata E-37
Maritimibacter alkaliphilus

description: The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed based on the DNA sequences of the orthologs using the Hierarchical Probe Design (HPD) algorithm. The array consists of 1,578 probes to 431 genes.

first: J

last: Rinta-Kanto

first: H

last: Bürgmann

first: S

last: Gifford

last: Sun

first: R

middle: P

last: Kiene

first: M

middle: A

last: Moran


title: NimbleGen Human p53 binding array (hg17)

status: Public on Aug 09 2010

city: Rehovot

first: Efrat

last: Lidor Nili

address: Herzel

country: Israel

institute: Weizmann Institute of Science

organism: Homo sapiens

manufacture_protocol:
see manufacturer's web site www.nimblegen.com
Annotation in this record based on NCBI human build 35 (hg17)


title: AGRF Environmental functional gene microarray (E-FGA)

city: St Lucia

first: Regina

last: Sintrajaya

state: Queensland

address: Mansfield Pl, Blg 62 John Hines Lvl 3

department: School of Biological Science

institute: The University of Queensland

organism: uncultured microorganism

description: Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities

manufacture_protocol: Amplification of cDNA clones using M13F/R primers, purification using Ethanol precipiation, and array manufacturing by spotting of PCR products onto array


title: NcodeTM Multi-Species miRNA Microarray V2

city: Hong Kong

first: Patrick

middle: YK

last: Yue

address: Waterloo Road

country: Hong Kong

institute: Hong Kong Baptist University

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: see manufacturer's web site


title: Human-mouse dual-species array HomoMus_v2

status: Public on Aug 04 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

organism:
Homo sapiens
Mus musculus

description: Customized Agilent array designed using eArray software

manufacture_protocol: Agilent 4x44K array protocol


title: NimbleGen_Rat_385K_Array

first: Christopher

last: Hamm

address: 2430 N. Halsted Street

department: Cancer Biology and Epigenomics

institute: Children’s Memorial Research Center

organism: Rattus norvegicus

description: Rat 385K array, 26,739 genes, 14 probes/target

first: Maria

middle: F

last: Bonaldo

first: Marcelo

middle: B

last: Soares


title: Applied Microarrays CodeLink Mouse Whole Genome Bioarray

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

institute: Institute for Medical Microbiology


title: Oxford Gene Technology Streptomyces coelicolor 4x44K format

city: Norwich

first: Chris

last: den Hengst

state: Norfolk

address: Colney

department: Molecular Microbiology

institute: John Innes Centre

organism: Streptomyces coelicolor

manufacture_protocol: Arrays consisted of 43798 60-mer oligonucleotide probes that match Streptomyces coelicolor sequences at average intervals of 198 bp.


title: LU/IBL_D.rerio_Agilent_44k_021626

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

organism: Danio rerio

manufacture_protocol: Agilent Ink Jet manufactured


title: Melon single feature polymorphism array v1.0 187K

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

institute: Agricultire Research Organization

organism: Cucumis melo subsp. melo

first: Amir

last: Sherman

manufacture_protocol:
Agilent SurePrint technology
Array was designed using melon ESTs deposited at www.icugi.org. Both catalog and custom microarrays are manufactured using a proprietary non-contact industrial inkjet printing process in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints up to 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide.


title: Human 50K Exonic Evidence-Based Oligonucleotide array

city: Nashville

first: Britney

last: Grayson

state: TN

address: MCN T-3219, 1161 21st Ave South

department: Microbiology and Immunology

institute: Vanderbilt University School of Medicine

manufacture_protocol: see www.microarrays.com


title: GRASP 16K version 2 (GB_ACC version)

city: Logy Bay

first: Jennifer

middle: Rejeanne

last: Hall

state: NL

address: 1 Marine Lab Rd.

department: Ocean Sciences Centre

institute: Memorial University of Newfoundland

organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

manufacturer: consortium Genomics Research on All Salmon


title: 23K Silkworm Genome Array

city: Shanghai

first: Ling

last: Tian

address: Fenglin Road 300

department: Institute of Plant Physiology and Ecology

institute: Chinese Academy of Sciences

organism: Bombyx mori

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Affymetrix Bacillus anthracis custom array_version 2 [B_anthracis]

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

organism: Bacillus anthracis

description: Affymetrix CDF, PROBE_TAB, and GIN files linked below.


title: Illumina GoldenGate mouse SNP Ube3a-Snurf/Snrpn region

city: Tsukuba

first: Koji

last: Numata

address: 3-1-1 Koyadai

institute: RIKEN

technology: oligonucleotide beads

first: Chihiro

last: Kohama

first: Kuniya

last: Abe

first: Hidenori

last: Kiyosawa

manufacture_protocol:
Illumina GoldenGate Assay was used.
See manufacturer's web site for more details.


title: UTHSC/Kotb Streptococcus pyogenes 2.3K v1

status: Public on Dec 01 2008

city: Wollongong

first: Andrew

last: Hollands

state: NSW

address: Northfields Ave

department: School of Biological Sciences

institute: University of Wollongong

organism: Streptococcus pyogenes

manufacturer: Molecular Resource Center, University of Tenessee Health Sciences Center

manufacture_protocol:
Each array consists of duplicates of 2,328 oligomers (70-mers) that represent all ORFs in M1 GAS, strain SF370 (GenBank accession# NC_002737) in addition to oligomers representing ORFs from prophages in strains MGAS8232 (GenBank accession# NC_003485) and MGAS315 (GenBank accession# NC_004070). The arrays also contained positive and negative controls of streptococcal ribosomal DNA and alien DNA (Stratagene), respectively.
This is a condensed version of the full array.


title: DKFZ Homo sapiens 8k BAC-array version 2

status: Public on Jan 12 2008

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter

manufacture_protocol: Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.


title: Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 1

status: Public on Aug 15 2009

city: Chicago

first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

organism: Arabidopsis thaliana

description: This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse A. thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along A. thaliana genome with ~35 bp resolution on both strands. The reference genome of the array design is Col-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR7.

first: Susanna

last: Atwell

first: Yu

last: Huang

first: Bjarni

last: Vilhjalmsson

first: Glenda

last: Willems

first: Matt

last: Horton

first: Dazhe

last: Meng

first: Alexander

last: Platt

first: Aaron

last: Tarone

first: Yan

last: Li

first: Wayan

last: Muliati

first: Mohammad

last: Amer

first: Ivan

last: Baxter

first: Benjamin

last: Brachi

first: Joanne

last: Chory

first: Caroline

last: Dean

first: Marilyne

last: Debieu

first: Juliette

last: de Meaux

first: Joseph

last: Ecker

first: Nathalie

last: Faure

first: Joel

last: Iskern

first: Jonathan

last: Jones

first: Todd

last: Michael

first: Adnane

last: Nemri

first: Fabrice

last: Roux

first: David

last: Salt

first: Chunlao

last: Tang

first: Brian

last: Traw

first: Detlef

last: Weigel

first: Joy

last: Bergelson

first: Magnus

last: Nordborg

manufacture_protocol: See manufacturer's web site