title: Illumina Genome Analyzer (Macaca fascicularis)

status: Public on May 31 2011

last: GEO

country: USA

organism: Macaca fascicularis

technology: high-throughput sequencing

distribution: virtual


title: NimbleGen Custom Rice Centromere Tiling Array (design:080925/080227)

status: Public on Nov 08 2011

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

organism: Oryza sativa

technology: in situ oligonucleotide

description: Genomic tiling array that covers four rice centromeres (Cen4, Cen5, Cen7, and Cen8) using the NimbleGen 3x720K array based on the NimbleGen HD2 platform.

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site


title: NimbleGen E.chaffeensis expression array (080428_Ehrchaf_JK_EXP_X4)

status: Public on Sep 06 2011

city: Galveston

first: Jeeba

middle: A

last: Kuriakose

state: TX

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

organism: Ehrlichia chaffeensis

description:
Five replicates of the genome were included per chip, with an average of 12 different 60-base oligonucleotides (60-mer probes) represented each open reading frame in the E. chaffeensis genome.  , unique probes were designed for 1031 ORFs of the 1158 ORFs, 1.18Mbp genome.
GenBank accession no. CP000236

manufacture_protocol: The arrays were manufactured using maskless, digital micromirror technology.  See manufacturer's website at http://www.nimblegen.com/.


title: NimbleGen Desulfovibrio vulgaris 385k array

city: Berkeley

first: Lara

last: Rajeev

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

description:
Includes genome sequence (Genbank AE017285.1) and plasmid pDV sequence (Genbank AE017286.1)
385k custom tiling array designed to examine the intergenic regions. The probes (50-mer) have 46 bp overlap in the intergenic regions and a 20 bp overlap in the coding regions
Design ID: 081029

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


title: Illumina Genome Analyzer II (Desulfovibrio vulgaris str. Hildenborough)

status: Public on May 26 2011


title: NimbleGen Custom Zebrafish aCGH Array

status: Public on Apr 16 2012

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

organism: Danio rerio

first: Woei-Chang

first: Richard

last: Bartfai

first: Rajini

last: Sreenivasan

first: Zijie

last: Lim

first: Laszlo

last: Orban

manufacture_protocol: Please visit NimbleGen website


title: febit Aspergillus nidulans FGSCA4 14k v1.0

status: Public on May 25 2011

city: Jena

first: Fabian

last: Horn

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI)

organism: Aspergillus nidulans

distribution: commercial

manufacture_protocol: One probe for each gene was synthesized on array. Provision of blank probes only consisting of one T used for background correction. Probes are longmers.


title: febit+HKI Aspergillus nidulans FGSCA4 10k v2.0


title: [MHC_MAP1_univ] Custom Affymetrix MHC Tiling Array

status: Public on May 23 2011

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

country: France

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7

organism: Homo sapiens

manufacture_protocol: See manufacturer's website


title: Exiqon miRCURY LNA microRNA Array, v.8.0 - all organisms (miRBase 14.0)

city: Cambridge

first: Matthew

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

country: United Kingdom

institute: MRC Cancer Cell Unit

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

technology: spotted oligonucleotide

description:
miRNA annotation based on Sanger miRBase 14.0.
LotNumberRange: 1008-1012


title: Affymetrix Human Promoter 1.0R Array [genome build GRCh37]

status: Public on Nov 14 2011

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
Custom probe annotation of Affymetrix Human Promoter 1.0R Tiling microarray.
Annotation based on genome build GRCh37 (NCBI build 37; hg19).
The data table contains only those probes that have a unique complete alignment to the genome, probes with multiple alignments or additional incomplete alignments (allowing 1 mis-match) were excluded.


title: Illumina Genome Analyzer II (Histophilus somni)

organism: Histophilus somni


title: Genotypic Designed 60mer Drosophila Whole Genome Microarray with 60,000 Features

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

organism: Drosophila melanogaster

first: Raja

middle: C

last: Mugasimangalam


title: NimbleGen Desulfovibrio vulgaris Hildenborough 2004K

status: Public on May 27 2011

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

manufacture_protocol: see manufacturer's website


title: ORNL Clostridium thermocellum Oligoarray

status: Public on May 24 2011

city: Oak Ridge

first: Babu

last: Raman

state: TN

address: One Bethel Valley Road

institute: Oak Ridge National Laboratory

organism: Acetivibrio thermocellus ATCC 27405

distribution: non-commercial

manufacture_protocol: DNA sequences for the 3163 C. thermocellum ATCC 27405 predicted protein-encoding genes were obtained from The Joint Genome Institute using sequence assembled in November 2003. Oligonucleotide probes that represented the whole genome of C. thermocellum were designed using the CommOligo software and were commercially synthesized without modification (MWG Biotech, High Point, NC) in 96-well plates. The concentration of the probes was adjusted to 100 pmol/JlL, transferred to 384-well printing plates in a final concentration of 50% dimethyl sulfoxide using a BioMek FX liquid handling robot (Beckman-Coulter, Fullerton, CA) and then spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI) in a dust-free clean room maintained at 21°C and 50% relative humidity. Spotted DNA was stabilized on slides by ultraviolet crosslinking using an Ultraviolet 1800 Stratalinker (Stratagene, La Jolla, CA) according to the slide manufacturer's instructions (Corning Life Sciences). Oligonucleotide probes originally designed based on the 2003 draft genome sequence were BLAST compared against the 2006 fully assembled genome to identify the corresponding open reading frames in the completed genome.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) custom CDF: HuEx10stv2_Hs_VEGAE.cdf (v10)]

description: Chip description file: HuEx10stv2_Hs_VEGAE.cdf (v10)

relation: Alternative to: GPL5188 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: NimbleGen Homo sapiens Custom HG18 Whole Genomne Tiling Array 3 of 4

status: Public on Aug 28 2011

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

description: Build: HG18, NCBI 36


title: NimbleGen Homo sapiens Custom HG18 Whole Genomne Tiling Array 4 of 4

description: Build: HG18, NCBI 36


title: SALSA 2 IFR Salmonella 8K Arrays

status: Public on May 20 2011

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. DT104
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Enteritidis
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

technology: spotted DNA/cDNA

first: Arthur

last: Thompson

first: Sacha

last: Lucchini

manufacture_protocol:
PCR product microarray of ORF's from S. Typhimurium LT2, S. Typhimurium SL1344, S. Typhimurium DT104, S. Enteritidis PT4, and S. Gallinarum 287/91. For the description of PCR amplification and printing procedures see:
Clements et al., (2002) PNAS 99(13): 8784-8789;
Nagy et al., (2006) Infect. Immun. 74(10):5914-5925


title: NimbleGen Homo sapiens Custom HG18 Whole Genomne Tiling Array 2 of 4

description: Build: HG18, NCBI 36


title: NimbleGen Cryptococcus H99 Whole Genome CGH array (12x135K)

city: Vancouver

first: Guanggan

last: Hu

email: hug@msl.ubc.ca, kronstad@msl.ubc.ca

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

organism: Cryptococcus neoformans H99

description:
Whole genome CGH array of Cryptococcus neoformans strain H99 (serotype A genome) but excluded centromere regions.
14 chromosomes tiled (int=100/win=33/mm=1). Final interval spacing: 133 bp (mean); 134 bp (median).


title: Agilent-018006 Canis familiaris CSL v1

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

organism: Canis lupus familiaris

description:
Modified dog array for CSL blood

Arrays of this design have barcodes that begin with 16018006 or 2518006.

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: Nimblegen Homo sapiens HG18 Expression Array (12x135k)

status: Public on May 22 2011

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description: This is a whole human genome array in 12-plex format provided by Roche Nimblegen. See manufacturer's website at http://www.nimblegen.com/.

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


title: Duke Operon Mouse v3.0 oligo array (Gene symbol version)

status: Public on Jul 03 2011

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

department: Neurobiology

institute: Duke University

organism: Mus musculus

description: Operon’s Mouse Genome Oligo Set (3.0) which contains 31,769 70-mer probes representing 24,878 genes and 32,829 transcripts (Operon, Huntsville, AL).

manufacture_protocol: Arrays were printed using an Omnigrid 300 arrayer by Genomic Solutions (Ann Arbor, MI) on Corning UltraGap amino-saline coated glass slides


title: NimbleGen Homo sapiens Custom HG18 Whole Genomne Tiling Array 1 of 4

description: Build: HG18, NCBI 36


title: Valencia yeast v9

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

organism: Saccharomyces cerevisiae

description: Nylon macroarray (7 x 11 cm) with 6144 positions: 6026 single spotted yeast ORF/non-ORF gene probes; 45 probes for rRNA controls and 15 probes for B. subtilis genes as spiked controls. Probes are PCR fragments comprising the whole ORF (5558 cases) or a 1000-bp fragment from the ORF 3' end (451 cases).

manufacturer: Seccion de Chips de DNA-SCSIE (University of Valencia)

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206 (PMID 15492934).


title: NimbleGen Cell Cycle promoter array

status: Public on May 21 2011

city: Stanford

first: Tiffany

last: Hung

address: 371 SERRA MALL

institute: Stanford University

manufacture_protocol: standard Nimblegen protocol


title: LC_MRA-1002_miRMouse_10.1_071219 (miRNA ID version)

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1.

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://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: Umea Lucidea array

city: Umeå

first: Mattias

last: Landfors

address: Umeå University

department: Clinical bacteriology

country: Sweden

institute: Umeå University

organism:
Pinus sylvestris
Mus musculus

description: The in-house produced cDNA-array contains 44 clones: 19 clones from mice, 4 clones from Pine (involved in photosynthesis) and 21 artificial clones from the Lucidea Universal ScoreCard (Amersham Bioscienses), where each clone was printed 480 times in 48 identically designed sub-grids.

manufacture_protocol: The clones were dissolved in 50% DMSO and printed using 2500K pins (Biorobotics) with a MicroGrid II 610 instrument (Biorobotics) on Ultra GAPS slides (Corning).  The array is spotted in 48 subarrays (4x12) with a 21x21 pattern within each subarray


title: Illumina Genome Analyzer (Candidatus Puniceispirillum marinum IMCC1322)

last: GEO


title: Illumina Genome Analyzer IIx (Manihot esculenta)

status: Public on May 19 2011

organism: Manihot esculenta


title: Invitrogen ProtoArray v5.0

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: spotted peptide or protein


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set34 [DESIGN_ID: 4105]

status: Public on May 17 2011

city: Madison

description: Set 34 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.

manufacture_protocol: see manufacturer's web site


title: febit Homo sapiens miRBase 13.0 plus

status: Public on May 18 2011

city: London

first: Adam

middle: Enver

last: Frampton

address: Hammersmith Hospital

institute: Imperial College

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: NimbleGen Mouse 2006-07-17_MM8Tiling_Set32 [DESIGN_ID: 4103]

description: Set 32 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set36 [DESIGN_ID: 4107]

description: Set 36 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set35 [DESIGN_ID: 4106]

description: Set 35 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set33 [DESIGN_ID: 4104]

description: Set 33 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set26 [DESIGN_ID: 4097]

description: Set 26 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set23 [DESIGN_ID: 4094]

description: Set 23 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set21 [DESIGN_ID: 4092]

description: Set 21 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set28 [DESIGN_ID: 4099]

description: Set 28 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set27 [DESIGN_ID: 4098]

description: Set 27 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set30 [DESIGN_ID: 4101]

description: Set 30 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set38 [DESIGN_ID: 4109]

description: Set 38 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set19 [DESIGN_ID: 4090]

description: Set 19 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set24 [DESIGN_ID: 4095]

description: Set 24 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: Eucalyptus Array #1

city: Canberra

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism: Eucalyptus nitens

description: Random Eucalyptus cDNA

first: Simon

last: Southerton

first: Iain

last: Wilson

manufacture_protocol: A cDNA library of genes expressed in differentiating xylem tissue from a vertical stem of E. grandis was constructed using the Stratagene lambda ZAP®II pre-digested vector kit (Stratagene, La Jolla, CA) with poly (A)+mRNA isolated by methods described previously (Southerton et al., 1998). The primary library was amplified before pBluescript phagemids were mass excised using the ExAssit/SOLR system (Stratagene, La Jolla, CA). Randomly picked phagemid colonies were cultured in a 96-well plate and the inserts amplified by PCR directly using forward, 5'-GTAAAACGACGGCCAGTG- 3' and reverse, 5'-GGAAACAGCTATGACCATG- 3' primers. The 100 ?l PCR reaction mixture contained 10 ?l of 10X PCR (-Mg2+) buffer, 2 ?l of 10 mM dNTP mixture, 5 ?l of primer mix (10 ?M each), 77.5 ?l of MilliQ water, 0.5 ?l of Taq DNA polymerase (5U ?l-1, LifeTechnologies, Rockville, MD) and 2 ?l supernatant 1 from overnight culture. Reactions were amplified on a 9600 GeneAmp PCR System (Perkin-Elmer, Foster City,  CA) using the following PCR amplification programme: 3 min denaturation at 95 °C, 34 cycles of 30 s at 94°C, 30 s at 45°C and 2.5 min at 72°C, followed by a 7 min extension at 72°C. The PCR products were purified using the TIGR's filtration protocol (Hegde et al., 2000). After washing twice with 100 ?l of MilliQ water, 16 ?l of 3 X SSC was added to each well and shaken vigorously for 10 minutes on a shaker to resuspend the DNA. Approximately 4,900 cDNAs were printed onto Superaldehyde glass slides (TeleChem, Sunnydale, CA) using a Bio-Rad (Hercules, CA) VersArray Chipwriter Pro with SMP 3 stealth microspotting quill pins (TeleChem, Sunnydale, CA). Each cDNA was spotted twice by different pins on a different area of the same slide. Glass slides were processed according to the TeleChem protocols. Cy3-and Cy5-labeled (Amersham Pharmacia) cDNA probes were generated using the two-step labelling method described by Schenk et al. (2000). Application of the probe to microarray slides, hybridization, and subsequent washes of the slides were performed according to Schenk et al. (2000). For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set20 [DESIGN_ID: 4091]

description: Set 20 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set37 [DESIGN_ID: 4108]

description: Set 37 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set18 [DESIGN_ID: 4089]

description: Set 18 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set17 [DESIGN_ID: 4088]

description: Set 17 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set25 [DESIGN_ID: 4096]

description: Set 25 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set16 [DESIGN_ID: 4087]

description: Set 16 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set31 [DESIGN_ID: 4102]

description: Set 31 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set15 [DESIGN_ID: 4086]

description: Set 15 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set22 [DESIGN_ID: 4093]

description: Set 22 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set13 [DESIGN_ID: 4084]

description: Set 13 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set29 [DESIGN_ID: 4100]

description: Set 29 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set14 [DESIGN_ID: 4085]

description: Set 14 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set12 [DESIGN_ID: 4083]

description: Set 12 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set11 [DESIGN_ID: 4082]

description: Set 11 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set10 [DESIGN_ID: 4081]

description: Set 10 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set08 [DESIGN_ID: 4079]

description: Set 8 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set09 [DESIGN_ID: 4080]

description: Set 9 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set05 [DESIGN_ID: 4076]

description: Set 5 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set06 [DESIGN_ID: 4077]

description: Set 6 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set07 [DESIGN_ID: 4078]

description: Set 7 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set04 [DESIGN_ID: 4075]

description: Set 4 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: Illumina Genome Analyzer (Aegilops tauschii)

status: Public on May 12 2011

organism: Aegilops tauschii


title: Agilent-015984 custom yeast 8x15k GE array

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description:
S. cerevisiae GE. reformat catalog probes on 8x15k

Arrays of this design have barcodes that begin with 16015984 or 2515984.

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 Mouse 2006-07-17_MM8Tiling_Set02 [DESIGN_ID: 4073]

description: Set 2 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: Agilent-022770 Macaca mulatta 951K rheMac2 TargetedRegionsRSmith

status: Public on May 11 2011

city: Buffalo

first: Omer

last: Gokcumen

state: New York

address: 109 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

organism: Macaca mulatta

description:
Targeted Regions with large backbone

Arrays of this design have barcodes that begin with 16022770 or 2522770.

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: Agilent Array ID 022715 (forward strand) and Array ID 022716 (reverse strand)

status: Public on May 16 2011

city: Cambridge

first: Vikram

last: Vijayan

state: MA

address: 52 Oxford Street, Room 440

institute: Harvard University

organism: Synechococcus elongatus PCC 7942 = FACHB-805

description: Agilent 1x244k


title: Illumina Genome Analyzer (Phaeodactylum tricornutum)

organism: Phaeodactylum tricornutum


title: 454 GS FLX (Capsicum annuum)

organism: Capsicum annuum


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set03 [DESIGN_ID: 4074]

last: Nimblegen Systems

description: Set 3 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: Illumina Genome Analyzer II (Oryza sativa Indica Group)

status: Public on May 10 2011

organism: Oryza sativa Indica Group


title: Invitrogen Ncode miRBase Microarray V2

status: Public on May 14 2011

city: Otsu,

first: hirotaka

last: yamamoto

state: Shiga,

address: Tsukinowa, Seta,

country: Japan

institute: Shiga University of Medical Science

manufacture_protocol: The NCode™ Multi-Species miRBase Microarray Kit V2 contains optimized probes targeting all of the known mature miRBases in mirBase 9.0 for human, mouse, rat, Drosophila, C. elegans, and zebrafish, spotted in triplicate on Corning Glymo epoxide slides


title: NimbleGen Mouse 2006-07-17_MM8Tiling_Set01 [DESIGN_ID: 4072]

description: Set 1 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.


title: FI SWEGENE H_v2.1.1 55K

city: Helsinki

first: Taru

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital

organism: Homo sapiens

manufacture_protocol: This platform is a condensed version of GPL5345 modified to fit the analyses. GPL5345 was used in the hybridizations and the raw data files reflect the uncondensed array. Arrays were produced by the Swegene DNA micro array resource center at Lund University by using probes from Operon. Probes were recovered in Corning Universal Spotting Solution and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics).


title: JCVI Aspergillus fumigatus 20K microarray Version 2

city: Delhi

first: Santosh

middle: Kumar

last: Upadhyay

state: Delhi

address: Near Jubilee Hall, Mall Road Delhi

department: Allergy and infectious Disesases

institute: Institute of Genomics and Integrative Biology

organism: Aspergillus fumigatus

description:
Aspergillus fumigatus strain Af293
Epoxy based slides with spotted 70 mer oligonucleotides, 2 spots for each target

manufacturer: J. Craig Venter Institute (Rockville, MD)

manufacture_protocol: 2QAF, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000; http://pfgrc.jcvi.org/index.php/microarray/array_description/aspergillus_fumigatus/version2.html


title: OSUCCC miRarray v3.0 [mature miRNAs only]

city: Columbus

first: Jeff

middle: J

last: Palatini

state: Ohio

address: 460 West 12th Ave.

institute: The Ohio State University

description: Only mature human miRNAs are represented.

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufactured 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 that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. 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: Illumina Genome Analyzer II (Synechococcus elongatus PCC 7942)


title: MM8 promter array 1 and 2

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

manufacture_protocol: see Nimblegen


title: Genotypic Technology designed Custom Human Promoter 244k ChIP-on-chip Array  (AMADID-019469)

status: Public on May 13 2011

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

first: Raja

last: Mugasimangalam


title: Phalanx Human OneArray (version 4.3)

status: Public on May 09 2011

city: Prague

first: Katerina

last: Stechova

address: V Uvalu 84

department: Paediatric

country: Czech Republic

institute: Charles University 2nd Medical Faculty

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: SABiosciences Human Dendritic and Antigen Presenting Cell PCR Array

status: Public on May 08 2011

city: Boston

first: Attila

last: Szanto

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

technology: RT-PCR

description:
DC-APC Array
SABiosciences RT² Profiler PCR Array.

manufacture_protocol: see manufacturer's website


title: SABiosciences Human Toll-like Receptor Signaling Pathway PCR Array

description:
TLR Array
SABiosciences RT² Profiler PCR Array.


title: Illumina Genome Analyzer IIx (Deinococcus gobiensis)

status: Public on May 05 2011

last: GEO

organism: Deinococcus gobiensis


title: miRMouse_9.0_UB_070209

status: Public on May 06 2011

city: Bristol

first: Liang-Fong

last: Wong

address: Whitson Street

institute: University of Bristol


title: SMD Print_1111

city: Stanford

first: Zhen

last: Wang

address: Campus Drive

department: Surgery

institute: Stanford University

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: Capital Bio mouse 32K oligonucleotide microarray

city: Beijing

first: Liuyan

last: Zhang

address: 4A Dutun Rd., Chaoyang District

country: China

institute: Institute of Psychology, Chinese Academy of Sciences

manufacturer: Capital Bio Corporation (Beijing, China)

manufacture_protocol: See the manufacturer's web site.


title: UW/NimbleGen_humangorilla_custom_dupsdels

status: Public on May 01 2011

first: Tomas

last: Marques-Bonet

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

organism:
Gorilla gorilla
Homo sapiens

first: Mario

last: Ventura

first: Claudia

middle: R

last: Catacchio

first: Can

last: Alkan

first: Saba

last: Sajjadian

first: Tina

last: Graves

first: Fereydoun

last: Hormozdiari

first: Maika

last: Malig

first: Carl

last: Baker

first: Lee

last: Choli

first: Emily

last: Turner

first: Lin

last: Chen

last: Kidd

first: Nicoletta

last: Archidicacono

first: Jay

last: Shendure

first: Richard

middle: K

last: Wilson

first: Evan

last: Eichler

manufacture_protocol: Experiments were performed according to the manufactures procedures.


title: SIPPE Cassava 44k v1.0

city: Shanghai

first: Jun

last: Yang

address: 300 Fenglin Road

institute: SIPPE

description: A total of 20,840×2 in situ synthesized 60-mer oligonucleotide probes plus 1264 positive control features and 153 negative control features were designed on the microarray.

manufacture_protocol: Design probes by E-array, In-Situ Synthesized Oligonucleotide using Agilent Inkjet.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray RefSeq Version 13.0.0]

status: Public on Feb 28 2011

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, HGU133Plus2_Hs_REFSEQ].

CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp

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


title: Illumina Genome Analyzer (Myotis pilosus)

status: Public on May 04 2011

last: GEO

organism: Myotis pilosus


title: EMBRAPA/Grattapaglia Eucalyptus 44K genotyping array v1.0

status: Public on Sep 18 2010

city: Gainesville

first: Leandro

middle: Gomide

last: Neves

state: FL

address: 2033 Mowry Road

department: Plant Molecular and Cell Biology

institute: University of Florida

organism: Eucalyptus

manufacture_protocol: Agilent 25 mers


title: EMBRAPA/Grattapaglia Eucalyptus 103K discovery array v1.0

status: Public on Sep 16 2010


title: MRA-1002_miRMouse_10.1_071219

status: Public on Jul 20 2010

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Mus musculus

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1.

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://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 Genome Analyzer II (Drosophila yakuba)

status: Public on Feb 17 2010

organism: Drosophila yakuba


title: miRXplore TM Microarray (867)

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 5892 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1374 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1374 miRNA sequences covered sequence verified miRNAs of the species human (859) mouse (622) and rat (428) as well as viral miRNAs (129) as deposited in the miRBase sequence database version 12.0. 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.

first: Bernhard

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: Illumina Genome Analyzer II (Drosophila ananassae)

status: Public on Mar 21 2011

organism: Drosophila ananassae


title: Illumina Genome Analyzer II (Drosophila virilis)

organism: Drosophila virilis


title: Illumina HiSeq 2000 (Drosophila ananassae)


title: Illumina HiSeq 2000 (Drosophila yakuba)


title: Agilent-017278 whole human genome custom 4×44k array [alternate hg17 annotation]

status: Public on Apr 08 2011

first: Taichun

last: Qin

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

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


title: PIQOR (TM) Stem Cell Microarray, human AS (780)

description: The PIQOR (TM) Stem Cell Microarray is composed of 946 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: S. Typhimurium LT2 genome microarray version 2

city: College Station

first: Bhimanagouda

middle: S

last: Patil

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

organism: Salmonella enterica subsp. enterica

manufacturer: Pathogen Functional Genome Resource Center

manufacture_protocol: Please refer to webpage http://pfgrc.jcvi.org/index.php/microarray/array_description/salmonella_typhimurium/version2.html


title: NCSU_chicken_JS3 (359 oligos)

status: Public on Apr 30 2011

city: Ste Anne de Bellevue

first: Bushansingh

middle: Shyam

last: Baurhoo

state: Quebec

address: 21111, Lakeshore Road

department: Animal Science

institute: McGill University

organism: Gallus gallus

description: Each well was spotted 3 times (side-by-side) in the same grid, and grids were replicated 4 times on each slide; therefore, each gene was spotted a total of 12 times on the array. From the 480 wells printed (resulting in 5760 spots), 359 had an actual oligo (312 from plate A and 47 from plate B) and 121 had only spotting solution. These spots were annotated as NA (empty wells) and were not included in the statistical analysis resulting in output files containing 4308 spots (359 oligos as 12 replicates).

first: Jean

last: de Oliveira

first: Shelly

last: Druyan

first: Christopher

middle: M

last: Ashwell

manufacture_protocol:
1.70-mer oligos synthetized by Operon Biothechnologies Inc. Oligos were resuspended in Tris buffer; 250 µM of each oligo was added to one well of one of two 384-well plates (A and B) and dried (312 oligos in plate A and 47 oligos in plate B).
2. Oligos were resuspended in Universal Spotting Solution (Corning, Inc)
3. Seal plates with Corning seals.
4. Shake plate at mid speed on plate vortexer for 1 minute.
5. Remove seal and place plate on appropriate place on VersArray ChipWriter array printer.
6. Place UltraGaps Amino-Silane Coated Slides on appropriate place on array printer
7. Run pin clean-up steps 5 times before start printing (using 1 pin)
8. Start printing run
9. Turn-off printer once run is completed
10. Take plate from printer, seal it with Corning seal and store it at -20 oC
11. Let slides dry on printer for 24h
12. Crosslink slides on UV over set to 6000 x 100 µJ/cm2, store slides on secator


title: D Steinhauser E.coli 4.4K Agilent Array

status: Public on Feb 13 2010

city: Potsdam

first: Szymon

last: Jozefczuk

address: Am Mühlenberg 1

institute: Max Planck Institute

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


title: LC_miRMouse_10.0_070802-MA1002

status: Public on May 29 2009

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.0


title: OSU-CCC Human and Mouse MicroRNA Microarray Version 3.0

status: Public on Jul 09 2010

first: Ewy

last: Mathe

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

organism:
Homo sapiens
Mus musculus

relation: Alternative to: GPL13415 (mature miRNAs only)


title: [UCDavis]-[Delta smelt]-[18240]-[V:1.2]

status: Public on Aug 18 2010

city: Davis

first: Richard

middle: Edward

last: Connon

state: CA

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

organism: Hypomesus transpacificus

description: ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED.

manufacturer: UCDavis School of Veterinary Medicine:APC

manufacture_protocol: Delta smelt microarray with 18,240 features; comprised of 8448 cDNA fragments printed in dulpicate (16,896) and 1344 control spots. Specific details: We constructed a delta smelt microarray using 8448 PCR amplified fragments from a normalized cDNA library. A cDNA library was created by ligating expressed sequence tags (ESTs) into p-BS plasmid vectors and cloned into chemically competent Escherichia coli cells (BioS&T Inc, Montreal, Quebec, Canada). Products were PCR amplified from 1µl bacterial suspension, and visualized on agarose gels.  Purified PCR fragments ranging in size from 1- 4kb, along with control spots, were pin-printed on glass slides in a 20 x 19 block format, with 48 blocks per microarray.  Microarrays were printed at the Array Core facility at Robbins Hall, UC Davis (now closed down). Microarray control spots included a number of hybridization tags comprised of a pooled PCR product from all spots on the array, H. transpacificus DNA, and four Spot Report System of alien PCR products from Arabidopsis thaliana; CAB, RCA, RBCL and LPT4 (Stratagene, USA).  Blank control spots consisting of 1x Nexterion buffer solution were printed interspaced with the above controls and as the last 12 spots in each block, and used to assess printing quality and potential cross contamination resulting from printing. Only genes that were differentially expressed following esfenvalerate exposure were sequenced.  Aliquots of respective bacterial colonies used to create the microarray were sequenced using standard M13 forward and reverse primers.  Sequencing was carried out at the CA&ES Genomic Facility, UC Davis.  Basic Local Alignment Search Tool; translated nucleotide (BLASTx) searches were performed on specific fragments that responded significantly to the exposure treatments. Sequences were annotated according to homologies to protein database searches using translated nucleotide sequences and direct nucleotide queries (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Homologies to other fish species were of primary consideration on gene annotation. Sequences were only annotated if they were found to have a BLASTx match with the expect value smaller than 1x10-5 and a score above 50. Accession number and species’ match were recorded with each annotation.


title: Illumina HiSeq 2000 (Drosophila virilis)


title: GUTHRIE_YEAST_SPLICINGARRAY_v20040216a

status: Public on Apr 04 2007

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

organism: Saccharomyces cerevisiae

manufacturer: Guthrie Lab, University of California, San Francisco

first: Jeffrey

middle: A

last: Pleiss

middle: B

first: Megan

last: Bergkessel

first: Christine

last: Guthrie

manufacture_protocol: Arrays were pin-printed using standard techniques.  All protocols are available at http://cat.ucsf.edu/equipment/arrayer/