title: Illumina Genome Analyzer II (Carollia brevicauda)

status: Public on Mar 29 2011

last: GEO

country: USA

organism: Carollia brevicauda

technology: high-throughput sequencing

distribution: virtual


title: IEM HAS Agilent-016392 Whole Mouse Genome microarray 4X44K

status: Public on Mar 31 2011

city: Budapest

first: Cecilia

last: Katalin

address: Szigony 43

department: Pharmacology

country: Hungary

institute: IEM HAS

organism: Mus musculus

technology: in situ oligonucleotide

description: This array represents a custom kit (4 slides instead of 5) of the commercial Whole Mouse Genome microarray 4X44K design. Arrays of this design have barcodes that begin with 2516392

distribution: custom-commercial

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


title: NImbleGen Chromosome 19 Tiling Array

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

organism: Homo sapiens

description:
Format: 385K
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 105

manufacture_protocol: see manufacturer's web site


title: Mouse Immunology 384 StellARray™ qPCR Array plates (# 00188202)

status: Public on Mar 28 2011

city: London

first: Diane

middle: Marylin

last: Scott

address: Du Cane Road

department: Immunobiology

country: United Kingdom

institute: Imperial College London

technology: RT-PCR

description: This GEO Platform record represents two different plates, one custom made by Bar Harbor labs and another commercially available. This is designated by the 'plate' column in the Platform table below.

manufacture_protocol:
Primers are arranged in a 384 well StellARray™ qPCR Array plates as dries samples.
10ul mastermix made from: Power Sybr green master mix, 1814.4μl DEPC treated water (Ambion) and 201.6μl cDNA diluted 1:10 with DEPC treated water, was added to each well.
The plates were sealed using an optical adhesive seal
The plates were briefly centrifuged and left at room temperature for 15min
The plates were run on a 7900HT sequence detection system using 384 well block and standard cycling conditions (95ºC 10mins followed by 40 cycles of 95 ºC for 15sec and 60 ºC for 1 min).


title: Mouse central chr7 tiling array

description:
Annotation in this record based on NCBI mouse build 36 mm8.
Genomic regions along distal chr7 from mm8, isothermal tiling oligos at 100bp
native array description file: 2006-07-17_MM8Tiling_Set16.ndf
native array description file: 2006-07-17_MM8Tiling_Set16.pos

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


title: Achaearanea tepidariorum CombiMatrix_CustomArray_12K-01

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

organism: Parasteatoda tepidariorum

description: Parasteatoda tepidariorum and Achaearanea tepidariorum are synonyms.

first: Yasuko

last: Akiyama-Oda

manufacture_protocol: Please refer to the manufacturer's website.


title: 454 GS FLX (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: Illumina Genome Analyzer II (Brassica rapa subsp. chinensis)

status: Public on Mar 30 2011

organism: Brassica rapa subsp. chinensis


title: Custom mouse distal chr7 tiling array

description:
Annotation in this record based on NCBI mouse build 36 mm8.
Genomic regions along distal chr7 from mm8, isothermal tiling oligos at 100bp
native array description file: 080121_Szabo_CoH_mm8_chr7_chip.ndf
native array description file: 080121_Szabo_CoH_mm8_chr7_chip.pos


title: NimbleGen Shigella sonnei 4467-gene oligo array

city: Shinjuku

first: Jiro

last: Mitobe

state: Tokyo

address: 1-23-1 Toyama

department: Bacteriology

institute: National Institute of Infectious Diseases

organism: Shigella sonnei Ss046

description: NimbleGen design name 2009-02-18_RDKK170_Sson_60mer, NimbleGen design ID 09NIDS41. A1:2 expression design for 4467 genes from Shigella sonnei Ss046 and associated plasmid pSs046 with 8 probes (60-mer) per gene. Each probe is replicated 2 times. The design includes random GC and other control probes.

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


title: UvA_MAD-mouse-22K-vs2.0

status: Public on Mar 09 2011

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Micro-Array Department, University of Amsterdam

manufacture_protocol:
1.Mouse Oligo libraries were bought from Sigma Genosys (Cat # MOULIBST & Cat # MOULIB384B)
2. Resuspend oligos in  25 ul 3 x SSC/1.5 M betain to 20 uM
3. Seal plates with Corning seals.
4. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
5. Centrifuge plates at 2000 rpm for 3 minutes.
6. Remove seals and place plate in appropriate location of a Lucidea MicroArrayer (Amersham Pharmacia BioSciences,Piscataway,Nj,USA)
7. Spot library on ultraGAPS slides (Corning)
8. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
9. Fix oligonucleotides by a heat treatment at 100C for a few seconds. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary.
10. Complete fixation with a UV treatment at 150 mjoule
11. Store arrays at dry and controlled location


title: NimbleGen Dog 137K 12plex CGH array (090529_CanFam_TN_CGH)

city: Seattle

first: Tom

last: Nicholas

state: WA

address: Foege Building S-250, Box 355065 3720 15th Ave NE

institute: University of Washington

organism: Canis lupus familiaris

description:
A total of 1987 CNV regions with previous evidence of containing a CNV were targeted with 136930 probes.

designfile: 090529_CanFam_TN_CGH.ndf
designname: 090529_CanFam_TN_CGH
designid: 10052
Genome build: canFam2


title: Illumina Genome Analyzer II (Desmodus rotundus)

organism: Desmodus rotundus


title: 454 GS FLX (Arabidopsis thaliana x Arabidopsis lyrata)


title: NimbleGen Dog Whole-Genome CGH 2.1M Tiling Array (CanFam2_CGH_HX1)

description:
gw2.1 genome-wide aCGH, with probes spread across the canFam2 genome assembly with 2164507 probes.

designfile: CanFam2_CGH_HX1.ndf
designname: CanFam2_CGH_HX1
designid: 7995
Genome build: canFam2


title: EBT_UA_Enchytraeus albidus_version1

city: Aveiro

first: Mónica

last: Amorim

address: Campus Universitário de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

organism: Enchytraeus albidus

technology: spotted DNA/cDNA

description: Platform is based on a non-model organism, so information unavailable for some of the genes from this library. Of the 480 genes, 348 have been sequenced and are listed in the Platform table with the respective accession number from GenBank.

manufacturer: Laboratory for Ecophysiology, Biochemisty and Toxicology, University of Antwerp

first: Amadeu

last: Soares

first: Wim

last: De Coen

manufacture_protocol:
The microarray is composed of a normalised cDNA library that followed the protocol of Shagin (Shagin et al., 2002). A pooled RNA sample - containing RNA aliquots from the individuals exposed to all the different exposure conditions - was used for the construction of the normalized cDNA library. The exposures included different concentrations of two chemical compounds and different soil types.
In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector specific primers (T7 and SP6 primers, Promega) and purified by an exosap reaction.
In preparation for spotting, cDNA-inserts of the clones were, amplified using adaptor specific primers (nested primers, Clontech), purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at ~150 ng/µl. A Qarray Mini Robot (Genetix) was used to spot each clone in triplicate onto aminosilane coated glass slides (Generoma microarray slides; Asper Biotech, Estonia). In addition, a set of artificial genes control genes (Lucidea Universal Scorecard, Amersham Biosciences, UK) was spotted in 20 replicates spread over each array: 10 calibration controls, 8 ratio controls and 2 negative controls. After rehydration and drying, the slides were fixated by UV-radiation at 300mJ (UV Stratalinker 2400; Stratagene, USA).


title: Mouse distal chr15 tiling array

description:
Annotation in this record based on NCBI mouse build 36 mm8.
Genomic regions along distal chr7 from mm8, isothermal tiling oligos at 100bp
native array description file: 2006-07-17_MM8Tiling_Set31.ndf
native array description file: 2006-07-17_MM8Tiling_Set31.pos


title: Operon Oligonucleotide Set Innate Immunity and Aspergillosis

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: The Platform data table reflects a condensed representation of the array's quadruplicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacturer: University of Wuerzburg microarray facility

first: Loeffler

last: Juergen

first: Kneitz

last: Susanne

first: Morton

last: Oliver

first: Mezger

last: Markus

first: Hornbach

last: Anke

manufacture_protocol:
1. Oligos are arrayed in 96 well plates. Each well contains 500 pmol of 55–70 nucleotides (nt) long oligos and consist of an 18–24 nt segment that targets  specific known human cytokine, chemokine and innate immunity genes
2. Add  3 x SSC + 1,5 M Betaine (in Rnase-free water) to 10 uM
3. Seal plates and wrap them in saran wrap
4. Let it resuspend in a humid chamber on a shaker (60 rpm) over night
5. Centrifuge plates at 2000 rpm for 3 minutes.
6. Rearray 10 µL into 384-well, V-bottom plates
7. Centrifuge plates at 2000 rpm for 3 minutes.
8. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 15 minutes before next cassette is needed to begin centrifugation.
9. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
10. Spots are printed in quadruplicates
11. For each subsequent preparation of these plates for a print run, add water to the wells instead of print buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during each dip.


title: NCode multi-species miRNA microarray V2

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

manufacture_protocol: see manufactuer's website


title: NimbleGen_Ppu_4-plex array v1.0

city: Tsukuba

first: yong

last: wang

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

institute: National Institute for Agro-Environmental Sciences

organism: Pseudomonas putida KT2440

description:
NimbleGen design name: 2007-11-29_GFC270_Pput_60mer_4plex
NimbleGen design ID: 6758
Native array description files:
2007-11-29_GFC270_Pput_60mer_4plex.ndf
2007-11-29_GFC270_Pput_60mer_4plex.ngd
Sample species: Pseudomonas putida KT2440

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


title: Rosetta Human Gene Expression Array

status: Public on Mar 01 2011

first: Xinwei

last: She

address: 401 Terry Ave. N

department: Molecular Informatics

institute: Rosetta Inpharmatics, Merck

description: Microarray design based on Johnson JM, et all, Science 2003, 302(5653):2141-2144

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals

manufacture_protocol: See manufacturer's website


title: Agilent Human custom chip-on-chip 2 x 105k tiling microarray AMADID: 024305

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

first: Bernard

middle: W

last: Futscher

manufacture_protocol: Agilent 60-mer SurePrint technology


title: Achaearanea tepidariorum CombiMatrix_CustomArray_12K-02

first: Hiroki

last: Oda

first: Yasuko

last: Akiyama-Oda


title: Febit GmbH Geniom Biochip MPEA Rattus norvegicus (Sanger miRBase version 14.0 September 2009)

city: Berlin

first: Nathanael

last: Raschzok

address: Augustenburger Platz 1

department: Department of Surgery; Campus Charite Mitte / Campus Virchow Klinikum

institute: Charité - Universitätsmedizin Berlin

organism: Rattus norvegicus

manufacture_protocol:
The febits biochip Geniom Biochip MPEA Rattus norvegicus was used for this analysis. 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: Agilent Arabidopsis 1 Microarray

city: Kumamoto

first: Mitsuhiro

last: Aida

address: 2-39-1 Kurokami, Chuo-ku

institute: Kumamoto University


title: Agilent-028485 Myk-Array v3b

status: Public on Nov 13 2011

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

organism: soil metagenome

description:
Agilent-028485 Myk-Array v3b 028483
Design ID: 028485
FuncPhyloArray v3b
A custom-made EcoChip microarray consisting of about 9000 probes targeting expressed fungals genes and about 5000 probes targeting the precursor-rRNA of different fungal lineages.
Source organisms of the array features are mainly soil fungi and plants.


title: BioFIG_Ophrys fusca_custom-made_spotted cDNA array

city: Lisboa

first: Filipa

middle: Isabel de Almeida

last: Monteiro

address: Ed. ICAT, Faculty of Sciences, Rua Ernesto Vasconcelos, Campo Grande

department: BioFIG

institute: Plant Systems Biology Lab

organism: Ophrys fusca

manufacture_protocol: Each clone printed twice in the same sub-grid.


title: Agilent custom Leishmania microarray v2

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

organism: Leishmania

description: Multispecies Leishmania microarray

manufacture_protocol: Agilent's 60-mer SurePrint technology


title: NimbleGen Custom Mouse Hox Tiling Array

status: Public on Apr 11 2012

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

description: Custom NimbleGen tiling microarrays were designed using http://genome.ucsc.edu/MM9 NCBI37. Co ordinates of Mouse Hox A, B, C and D clusters, and several other genes were included in the design.  For genes other than Hox clusters, we have included 2 KB upstream TSS and 2KB downstream TES. We have chosen probes that may match up to 10 places in the genome as necessary to fill gaps in coverage; average probe spacing is 46 bases; four copies of each probe to be placed on the array. For details about designing and manufacture http://www.nimblegen.com/

last: Marulasiddappa

first: Ragnhild

last: Eskeland

manufacture_protocol: Nimblegen manufacture protocol


title: Affymetrix Escherichia coli full sequence array (EcFS) [EcFS_1, EcFS_2, and EcFS_3]

first: Bei-Wen

last: Ying

address: 1-1-1 Tennoudai

institute: University of Tsukuba

organism: Escherichia coli

description: A high-density DNA microarray (Ono et al, 2008; Suzuki et al, 2007) covering the whole genome of E. coli W3110 strain (GenoBase, http://ecoli.naist.jp/GB6/search.jsp) was utilised. Both strands of the genome were alternately tiled at single-base resolution using 21-mer perfectly matching and three mismatching probes. A library consisting of a total of 18.6 million probes was arranged on three GeneChips for microarray analysis, covering four types of probe throughout the 4.6-Mb E. coli genome. One of three GeneChips was used here for transcriptional analysis.


title: Illumina Genome Analyzer (Laccaria bicolor; Populus tremuloides)

status: Public on Mar 24 2011

last: GEO

organism:
Populus tremuloides
Laccaria bicolor


title: SAGE:17:NlaIII:Thalassiosira pseudonana CCMP1335

status: Public on Mar 23 2011

organism: Thalassiosira pseudonana CCMP1335

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Thalassiosira pseudonana CCMP1335 using NlaIII as an anchor enzyme.


title: NIH Taqman Mouse MicroRNA Array

first: Kasey

middle: C

last: Vickers

address: 10 Center Dr. Bldg. 10 8N222

department: National Heart, Lung and Blood Institute

institute: National Institutes of Health

organism: Mus musculus


title: NIH Taqman Human MicroRNA Array

organism: Homo sapiens


title: SMD Print_607

status: Public on Mar 22 2011

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

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: NIH Taqman Human MicroRNA Array v.2


title: AB SOLiD System 3.0 (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: SMD Print_435


title: Agilent_Dm_5.1_440K_tiling

status: Public on Mar 25 2011

city: Durham

first: David

last: MacAlpine

state: NC

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

organism: Drosophila melanogaster

description: tiling array for modENCODE. Average probe spacing of 448 bp for Drosophila genome (5.1).

manufacture_protocol: Agilent Technologies


title: TaqMan(r) Array Human MicroRNA B Cards v2.0

status: Public on Mar 26 2011

city: Milano

first: James

middle: F

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare

manufacture_protocol: See manufacturer's website (http://www.appliedbiosystems.com/).


title: MRA-1037_miRFishes_14_SHOU

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Coelacanthimorpha

description: Custom miRNA microarray targeting the mature miRNAs of Fish (as of miRBase 14) and custom probes

first: C

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 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: SMD Print_146


title: SMD Print_1239


title: SMD Print_244


title: SMD Print_433


title: Operon Library Version MEEBO Mus musculus v1.05

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: The supplementary file 'GPL13275_A-MEXP-220.adf.txt' represents the design file for this array.

manufacture_protocol: The Qiagen-Operon (Alameda, CA) mouse 70-mer oligonucleotide library, version 3.0, representing 31,769 annotated genes were suspended in 3X SSC and printed at 22C and 65% relative humidity on aminosilane-coated Cel Associates slides (#CSA-100C, Pearland, TX) using a high-speed robotic OmniGrid machine (GeneMachines; San Carlos, CA) with Stealth SMP3 pins from Telechem (Sunnyvale, CA). Spot volumes were 0.5 nl and spot diameters 75-85 mm. The oligonucleotides were crosslinked to the slide substrate by exposure to 600 mJ of ultraviolet light.


title: CATMA Arabidopsis 30K V3 TAIR V9 spotted cDNA array

city: Norwich

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

organism: Arabidopsis thaliana

manufacture_protocol: Arabidopsis GST products were produced by PCR as part of the CATMA Project (see Catma website www.catma.org. These were spotted using a Biorobotics TASII instrument using 24 pins split pins with a 26 by 26 grid pattern for each pin. Slides used were aminosilane treated Corning UltraGapII slides. Slides were checked for quality post spotting through staining each slide was bar coded and tracked individually.


title: TAGC Homo sapiens 9k (HuSG9k) v1

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: Nylon based microarray with cDNA probes

manufacture_protocol: Briefly, HuSG9k is a human cDNA nylon chip designed from IMAGE clones. The microarray contained 9216 spots. Among 8682 genes, 100 genes are duplicated with another clone. Four hundred and thirty four probes served as controls. The microarray design was not enriched in specific pathways. Genes with known functions were selected when predicted genes or genes with unknown function were discarded. Probes were selected by bioinformatics analysis to match the 3' end of the major transcripts of each gene (Microarray Quality Control (MiQC), TAGC, INSERM U928; Marseilles, France). PCR products were spotted onto nylon membranes (Hybond-N+, Amersham) with a MicroGrid II arrayer (Affymetrix, Santa Clara, CA, USA). PCR amplification products of selected clones were 1 500 bp length on average. The robot used a print head of 16x4 arrangement of print tips. Each tip printed 144 spots in a 12x12 grid. Further details on the HuSG9k microarray are available on the TAGC website (http://tagc.univ-mrs.fr/).


title: Illumina Genome Analyzer II (Drosophila simulans)

status: Public on Mar 21 2011

organism: Drosophila simulans


title: TaqMan(r) Array Human MicroRNA A Cards v2.0


title: University at Buffalo Illumina MouseWG-6 v2.0 expression beadchip (Gene version)

city: Buffalo

first: Yingru

last: Liu

address: 3435 Main Street

institute: University at Buffalo

technology: oligonucleotide beads

manufacture_protocol: see manufacturer's website


title: Salmonella typhimurium/typhi version 8

status: Public on Mar 20 2011

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description:
This is a condensed template of duplicated features of PFGRC/JCVI Salmonella typhimurium/typhi version 8 microarray.
For full template information please refer : http://pfgrc.jcvi.org/index.php/microarray/array_description/salmonella_typhimurium/version8.html
The GAL Annotation File is linked as a Supplementary file at the foot of the record.

manufacture_protocol: Microarray Version - 8; Number of Grids - 48; Element Type - 70mer Oligonucleotide; Surface Coating – Aminosilane; Oligonucleotides Designed -5967; Replicate Oligo Printings - 2x; Controls - 500 Arabidopsis thaliana 70mers; 10 Arabidopsis thaliana amplicons.


title: TaqMan® Array Human/Mouse MicroRNA Panel (custom early version)

first: Christopher

middle: Paul

last: Arnold

address: 269 Campus Drive, CCSR building, Room 3205B

department: Microbiology and Immunology

organism:
Homo sapiens
Mus musculus


title: NimbleGen Human 385K x1 for 13 regions of HG18

status: Public on Mar 19 2011

city: Dublin

first: Ana

last: Barat

state: Dublin

address: Collins Avenue

department: School of Computing

country: Ireland

institute: Dublin City University

description:
Human genome build: HG18, NCBI36
Tiled at i55w15 (avg 70bp spacing), 2 copies of each probe on the array.

Native array description file:090512_Vassetzky_HG18_regions_ChIP.ndf
Native array description file:090512_Vassetzky_HG18_regions_ChIP.pos

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


title: Illumina HiSeq 2000 (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: Peking University Chicken miRNA 4k array

status: Public on Mar 18 2011

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

country: China

institute: Peking University

organism: Gallus gallus

description: Arrays contained 1721 DNA probes, including a non-redundant set of probes complementary to 440 known chicken miRNAs, 78 known chicken miRNA* and 1124 unknown chicken small RNAs from our deep sequencing data (denoted as 'nrxxxx', the corresponding sequences can be found in the raw data file), as well as probes for 78 predicted chicken snoRNAs and positive control probes for chicken U6 snRNA. Negative controls to normalize the data with low-density signals were also included.

manufacture_protocol: see manufacturer's website www.lcsciences.com,


title: 3D-Gene Mouse miRNA Oligo chip V14.1.0.1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

distribution: commercial

manufacture_protocol: See manufacture's web site


title: Illumina Genome Analyzer II (Ptomaphagus hirtus)

organism: Ptomaphagus hirtus


title: Affymetrix Chicken Genome Array [GgChicken_ENTREZG10]

relation: Alternative to: GPL3213 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Drosophila mojavensis)

organism: Drosophila mojavensis


title: Illumina HiSeq 2000 (Drosophila simulans)


title: Illumina Genome Analyzer II (Labeo rohita)

status: Public on Mar 16 2011

organism: Labeo rohita


title: Tufts Homo sapiens 21K V2.1.2 + v2.1.4

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

institute: Medical College of Wisconsin

description: GPL13290_Operon_human_V2.1.4.xls.gz file contains oligonucleotide sequences for v2.1.4 only.

manufacturer: Operon and Tufts University Expression Analysis Core facility

manufacture_protocol: Operon v2.1.2 plus v2.1.4 spotted onto single chips by the Tufts University Microarray Core facility.


title: Princeton Biocomplexity Project, BC008 and BC009 arrays

status: Public on Mar 17 2011

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

organism: synthetic construct

description: The arrays contain three sets of probes for different applications (rbcL and nitrate reductase (NR) from phytoplankton, and amoA from ammonia oxidizing bacteria).  The paper to which this submission relates, and the experiments reported in it, used only the NR probe set. See linked sequence list for additional details.

manufacture_protocol: 90-mer oligonucleotides, spotted using DiRisi type arrayer


title: Illumina Genome Analyzer (Cordyceps militaris)

last: GEO

organism: Cordyceps militaris


title: Rinn Sabeti P. falciparum Tiling 385k v1.0

city: Cambridge

first: Kate

middle: Mariel

last: Broadbent

state: MA

address: FAS Center for Systems Biology Northwest Building, room 469 52 Oxford Street

department: Systems Biology

institute: Harvard University

organism: Plasmodium falciparum

description: PlasmoDB v5.5 (www.plasmodb.org)

manufacture_protocol: The design fills 366479 probes on the array and targets the Watson (+) strand of chromosomes 2, 4, 7 and 9 and partial chromosomes 3:106138‐147339, 5:947885‐end, and 12:start‐66805. Probes are variable length oligonucleotides, averaging 55 bp each. Median probe spacing is 12 bp. Probe sequences were screened for excessive cross hybridization to 3D7 sequence: any probes with more than five close SSAHA matches were eliminated.


title: Affymetrix Plasmodium falciparum PFSanger Genechip tiling array

city: Rockville

first: Hongying

last: Jiang

address: 12735 Twinbrook Parkway

institute: NIAID/NIH

description:
Chip has only perfect-matched individual probes (2.5 million/chip).

The CDF files are based on probe locations on the chromosome.
The 'GPL11265_probe_level_annotation.txt' file contains probe-level annotation, including probe sequences.

first: Vivek

last: Gopalan

first: Martine

last: Zilversmit

first: Sudhir

last: Varma

first: Vijayaraj

last: Nagarajan

first: Jian

first: Jianbing

last: Mu

first: Karen

last: Hayton

first: Bruce

last: Henschen

first: Ming

last: Yi

first: Robert

last: Stephens

first: Gilean

last: McVean

first: Philip

last: Awadalla

first: Thomas

middle: E

last: Wellems

first: Xin-zhuan

last: Su

manufacture_protocol: See Affymetrix website.


title: Illumina Genome Analyzer (Macaca mulatta)

status: Public on Mar 10 2011

organism: Macaca mulatta


title: NRC-BRI Human HEEBO 39K array

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

organism: Homo sapiens

manufacturer: National Research Council Canada - Biotechnology Research Institute

manufacture_protocol:
Oligonucleotides of the HEEBO Genome Set were acquired from Invitrogen (http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Amplification-and-Expression-Profiling/Oligonucleotide-Design/HEEBO-and-MEEBO-Genome-Sets.html).
Oligonucleotides were resuspended at 22 µM concentration in 50% DMSO and spotted on Corning Ultragaps slides with a BioRad ChipWriter Pro microarray spotter equipped with 48 SMP3 pins (Telechem ArrayIt). UV crosslinking (600 mJ) was performed in a Stratagene UV Stratalinker.


title: [CentXbaAv2] Affymetrix Human CentXbaAv2 SNP Array

city: Wako-city

first: Kazuo

last: Yamada

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Brain Science Institute

description:
Affymetrix Early Access 50KXba array.

These arrays are the same as the commercial Mapping 100K arrays with the exception of some the probes being masked out. The data obtained from Affymetrix Early Access 50KXba and 50KHind arrays can be converted to Mapping 100K arrays by filtering out the rejected SNP probe IDs on Early Access array and converting the SNP IDs to Mapping 100K SNP IDs.


title: [CentHindAv2] Affymetrix Human CentHindAv2 SNP Array

description:
Affymetrix Early Access 50KHind array.

These arrays are the same as the commercial Mapping 100K arrays with the exception of some the probes being masked out. The data obtained from Affymetrix Early Access 50KXba and 50KHind arrays can be converted to Mapping 100K arrays by filtering out the rejected SNP probe IDs on Early Access array and converting the SNP IDs to Mapping 100K SNP IDs.


title: Agilent-031422 S_pneumoniae_CGH

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus pneumoniae

description: Arrays of this design have barcodes that begin with 16031422 or 2531422.. 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: SMD Print_1703 Saccharomyces cerevisiae cpce

city: Stanford

first: Dan

last: Klass

state: CA

address: 259 Campus Drive Beckman Rm 439

department: Biochemistry

institute: Stanford University

organism: Saccharomyces cerevisiae

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


title: Agilent-030010 Genotypic Technology designed Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE Microarray V2

status: Public on Mar 11 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

first: Raja

last: Mugasimangalam


title: Agilent-030009 Genotypic Technology designed Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE Microarray V1


title: University of Groningen Lactococcus lactis MG1363 amplicon/oligo 2.6K

status: Public on Mar 12 2011

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Lactococcus cremoris subsp. cremoris MG1363

technology: mixed spotted oligonucleotide/cDNA

last: de Jong

first: Siger

last: Holsappel

manufacture_protocol: Standard spotting protocol on MicroGrid


title: BlueChip-Bovine_V1.2

city: Quebec

first: Claude

last: Robert

address: Pavillon Comtois

department: Animal Sciences

institute: Laval University

organism: Bos taurus

manufacturer: Laval University Laboratory of animal genomics

manufacture_protocol: Templates of a set of candidates isolated from a collection of 4 subtracted cDNA libraries were amplified by PCR. The amplicons (of 450 bp on average) were purified to remove excess primers and free nuleotides and the remaining DNA was used as the source of DNA to fabricate the microarray. DNA was diluted in DMSO to increase surface tension and deposition was performed using a Vertel arrayer (now VerArray from BioRad) using solid pins. Each spot was duplicated and duplicates were replicated (4 spots for each target DNA). Quality of printing was determined by terminal transferase (TdT) assay.


title: Agilent-030831 Genotypic Technology Pvt. Ltd. custom Listeria monocytogenes J0161 8x15k array

organism: Listeria monocytogenes J0161

description: Genes taken from Listeria monocytogenes J0161 Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)


title: SMD Print_1587 Saccharomyces cerevisiae CPBZO8


title: SMD Print_1478 yeast protoarray YA104704

technology: spotted peptide or protein

manufacture_protocol: not provided


title: RN4 NR3C1 locus for ChIP (Agilent-020085)

status: Public on Mar 09 2011

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

organism: Rattus norvegicus

description: Agilent high-density ink-jet

manufacture_protocol: The oligonucleotide microarray is composed of 45220 45-60mer oligonucleotides from the Agilent's eArray ChIP probe database.


title: Arizona Arabidopsis Oligonucleotide Microarrays Version 3.0

city: Saskatoon

first: Raju

last: Datla

state: SK

address: 110 Gymnasium Place

institute: NRC-PBI

organism: Arabidopsis thaliana

manufacture_protocol: The arrays were printed using the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0. This set comprised 29,000 oligonucleotides. The print format comprises a single array printed using 48 pins.  The array contains 12 metarows and 4 metacolumns, with the subarrays containing 25 columns and 26 rows with a spacing of 170 x 165 microns.


title: Illumina Genome Analyzer II (Schizosaccharomyces japonicus)

status: Public on Mar 08 2011

last: GEO

organism: Schizosaccharomyces japonicus


title: RN4 NR3C1 locus for ChIP (Agilent-018263)

description: Agilent high-density ink-jet


title: Illumina Genome Analyzer (Rickettsia conorii str. Malish 7)

status: Public on Mar 02 2011

organism: Rickettsia conorii str. Malish 7


title: SMD Print_1531 yeast protoarray YPROT2


title: University of Alberta Escherichia coli 3x6K microarray

city: Edmonton

first: Michael

last: Gänzle

address: 4-10 Ag/For Centre

department: AFNS

institute: University of Alberta

organism: Escherichia coli

manufacturer: Microarray and Proteomics Facility, Dept. of Biological Sciences, U Alberta, Edmonton, Canada

first: Anthony

last: Cornish

manufacture_protocol:
The E. coli slide produced contains 5,978 oligos and a control set of 12 positive and 12 negative controls in a 4 by 4 block of sub-arrays which are printed in triplicate filling the slide surface with a total of 19086 spots printed at 200 um spacing in both the horizontal and vertical direction.

The Oligos have been dissolved to a final concentration of 18.75 uM in 150 mM NaPO4 buffer (pH 8.7) prior to printing. The slides used are Corning Epoxide slides which have been chosen for ease of use, low background, and consistantly exceptional results.

The Operon E. coli Genome Oligo Set version 1.0 consists of 5,978 70mer probes representing three strains of E. coli. The number of open reading frames represented is as follows: 4,289 ORF's in K12, 5,029 ORF's in O157:H7 (EDL933), and 4,836 ORF's in O157:H7 (Sakai). All 5,978 probes are designed within ORFs from both clones and predicted ORF's. For this probe set design, Operon employed its state-of-the-art methods and proprietary software.

All probes are Tm normalized to 75oC (+/- 5oC) and have a 5' amino linker.


title: Funtional Gene Array for Bioleaching Microorganism Community

city: changsha

first: xueduan

last: liu

address: lushan south road

institute: central south university

organism: unidentified microorganism


title: UNIFRBIO3 Chlamydomonas reinhardtii 10K v1.0

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

organism: Chlamydomonas reinhardtii

manufacture_protocol: Agilent 8x15 CustomArray


title: Agilent-021827 Human miRNA Microarray (V3) (Probe Name version)

status: Public on Mar 14 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies


title: BrownUniversity/FairbrotherLab Agilent-019800 Human 2x105K OSN_Validation tiling array

status: Public on Mar 03 2011

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St

department: MCB

institute: Brown University

description:
Custom tiling oligonucleotide 'detection microarray' was designed to be complimentary with the 'synthesized array' oligonucleotide pool used in MEGAshift assay.
All coordinates are from the hg17 genome.

manufacture_protocol: see manufacture's protocol at http://www.agilent.com/


title: SABiosciences Mus musculus RT-PCR 384 (PAMM - 3803E)

city: Bethesda

first: O M Zack

last: Howard

state: MD

address: 6701 Rockledge Dr.

department: DBIB

institute: NIH/CSR

organism: Mus musculus

manufacture_protocol: see manufacturer's website


title: Agilent-025096 Genotypic Technology designed Custom Xanthomonas oryzae 8x15k Gene Expression Profiling Microarray

status: Public on Mar 05 2011

organism: Xanthomonas oryzae

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

manufacture_protocol: Refer to www.opengenomics.com


title: RASTA Rattus norvegicus 0.3 k ver. 2

status: Public on Mar 01 2011

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite

manufacturer: LFGC, Charité Universitaetsmedizin Berlin, Germany

first: Iwona

last: Stelniec

manufacture_protocol:
The Ras signaling target array was designed and produced as described (Tchernitsa et al., 2005). Briefly, we selected 121 genes recovered from subtracted cDNA libraries representing sequences differentially expressed in parental and KRAS-transformed ROSE 199 cells (Tchernitsa et al., 2004). In addition, we selected genes from subtracted libraries representing sequences differentially expressed in normal 208F fibroblasts and the HRAS-transformed derivative FE-8 (Zuber et al., 2000). Previously described Ras pathway targets and 13 different genes described as housekeeping 20 genes in many different tissues and cell lines were included to permit normalization of hybridization intensities on microarrays. The total number of gene probes is 329 on the array.

Unmodified 70-mer DNA oligonucleotides were chosen as probe sets for the array. The oligonucleotide design was performed with software available on the web (http://oligo.lnatools.com/expression/) using the following parameters: option for LNA frequency=0, melting temperature between 74°C and 76°C, GC content between 45-55%, absence of strong secondary structures and proximity to 3’ end of coding sequence. Oligonucleotides were synthesized at Illumina, Inc (San-Diego, USA) at the 50 nmol scale. Super Frost glass slides (Menzel GmbH, Braunschweig, Germany) were soaked in 200 ml of washing solution containing 80 ml of 5M NaOH and 120 ml of 95% ethanol and agitated by a magnet stirrer for 5-6 h. Slides were washed 10-times with 200ml of ddH2O, incubated for 30 min on a shaker with poly-L-lysine solution (20ml of poly-L-lysine, Sigma-Aldrich, St. Louis, USA, mixed with 160 ml of ddH2O and filtered) and again washed 10-times with 200 ml of ddH2O. Afterwards, the remaining washing solution was removed by centrifugation of slides in a microarray centrifuge (Telechem, Sunnyvale, USA) and the slides were dried in an incubator for 2 h at 45°C. The oligonucleotides were adjusted to a concentration of 20µM in 3xSSC/0.01% SDS buffer and spotted using a MicroGrid compact microarrayer (Genomic Solutions, Ann Arbor, USA) equipped with MicroSpot 2500 quill pins. The pins have a diameter of 100µm and typically deliver spot diameters of 180µm. Microarrays were printed at a relative humidity of 50 - 60%. Pins were rinsed twice in distilled water between each probe aspiration/dispense cycle. Each of the 329 oligonucleotides was spotted tree times at a different location on the slides. After printing, microarrays were re-hydrated twice by placing them over boiling water for five sec each. Then each array was snap-dried on a hot plate (90°C) for 10 sec (DNA side 21facing upwards). Slides were cross-linked with an intensity of 60mJ (UVC-500 crosslinker, Hoefer, Inc, USA). Afterwards, slides were incubated in blocking solution (3.2 g of succinic anhydride mixed with 200ml of N-methyl-pyrolidone and 4.45 ml of 1M sodium borate) for 20 min on an orbital shaker, rinsed three-times with ddH2O and dried by centrifugation.


title: Illumina Genome Analyzer (Phalaenopsis aphrodite subsp. formosana)

organism: Phalaenopsis aphrodite subsp. formosana


title: RNG-MRC_HU25K_HsO2A

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

organism: Homo sapiens

description: Same DNA sequence probes in GPL11624, but updated gene symbols and varying number of replicate probes.

manufacture_protocol: spotted DNA/cDNA


title: Exiqon Mus musculus miRNA array [DesignedForVersion: miRBase ver.9.2, CurrentVersion: miRBase ver.10.0]

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 421 Curie Blvd

department: Medicine

institute: Univeristy of Pennsylvania

manufacture_protocol:
See manufacturer's website: http://www.exiqon.com/array
miRBase_DesignedForVersion=miRBase ver. 9.2
miRBase_CurrentVersion=miRBase ver. 10.0


title: Agilent-017159 Genotypic custom 60-mer oligonucleotide multibacterial microarray

first: Genotypic

last: technology

organism: synthetic construct

description: We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph),  biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected.  Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.

first: Raja

last: Mugasimangalam

first: Priya

last: Karthick


title: RIKEN BRC Human 11K Microarray Platform for Sense-AFAS Transcripts

city: Fujisawa

first: Rintaro

last: Saito

address: 5322 Endo

institute: Keio University

first: Keisuke

last: Kohno

first: Yuki

last: Okada

first: Yuko

last: Osada

first: Koji

last: Numata

first: Chihiro

last: Kohama

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Akio

last: Kanai

first: Hiroshi

last: Yasue

first: Soichiro

last: Murata

first: Kuniya

last: Abe

first: Masaru

last: Tomita

first: Nobuhiro

last: Ohkohchi

first: Hidenori

last: Kiyosawa

manufacture_protocol: Custom


title: Agilent Manduca sexta 37K

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

organism: Manduca sexta


title: RNG-MRC_HU25K_HsO4E

first: Yvan

last: Devaux


title: NimbleGen human HG18 whole genome aCGH plus custom probes

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
Annotation in this record is based on NCBI human genome Build 36 (UCSC hg18), 4633 custom-designed probes which cover the gene targeting construct and the reprogramming plasmid vectors.

The original whole-genome-tiling design has a resolution of 5 kb over the entire human genome, whereas our custom fine-tiling design can detect 200 bp CNV regions.

Native array description files:
100319_HG18_JN_CGH_HX1.ndf
100319_HG18_JN_CGH_HX1.pos

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


title: UNC-CH_Yeast Whole-genome Array (PCR-based)

city: Buffalo

first: Michael

last: Buck

address: 701 Ellicott St

institute: SUNY at Buffalo

organism: Saccharomyces cerevisiae

description: Whole-genome microarrays with PCR-amplified products represent ORFs, intergenic regions, and other noncoding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The noncoding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. This platform covers several print runs, in which print plates were arranged in different orders.

middle: J

first: Jason

last: Lieb

first: Sean

last: Hanlon

manufacture_protocol: see Iyer et al. 2001, Nature 409: 533-538


title: HMS/Somero-Mytilus-105K Agilent-v1.0 salinity stress

status: Public on Jan 10 2011

city: Pacific Grove

first: Brent

middle: L

last: Lockwood

address: 120 Oceanview Blvd.

department: Biology

institute: Hopkins Marine Station of Stanford University

organism:
Mytilus californianus
Mytilus galloprovincialis

description:
Agilent-019153

To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.5 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. Only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses.

This is the same microarray platform as GPL9676 HMS/SomeroLab-Mytilus-105K array-v1.0, but the probe data are uploaded here separately due to the increased number of probes that had good hybridization in this study. This discrepancy was due to our stringent quality control that removed bad probes from the dataset and the fewer number of samples in this study (36 arrays in this study vs. 84 arrays in the previous study (Lockwood et al. 2010, Journal of Experimental Biology, 213, 3548-3558)).

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

manufacture_protocol:
Approximately 26,000 publicly available ESTs from M. californianus (ES7325872 - ES738966; ES408175 - ES387463;(Gracey et al., 2008)) and M. galloprovincialis (AJ623313  - AJ626468; AJ516092 - AJ516921; (Venier et al., 2003)). SSH to enrich for transcripts expressed in response to various stressors.

Sequences for each species were separately screened for vector contamination, clustered, assembled, and loaded into a PostgresQL database using the PartiGene bioinformatics pipeline (Parkinson et al., 2004), yielding a total of 12,961 and 1,688 putative gene transcripts (clusters) for M. californianus and M. galloprovincialis sequences, respectively. Clusters were annotated for identity against the UniRef 90 protein database using NCBI Blast, with an e-value cutoff of 10-8. Clusters were also annotated for gene ontology (GO), enzyme classification (ECC), and gene pathway (KEGG) using the program annot8r (Schmid and Blaxter, 2008), again with an e-value cutoff of 10-8.  Long oligo (60-mer) probes were designed against the M. californianus clusters using the probe design program YODA (Nordberg, 2005) under default parameters, with a maximum of 5 probes per cluster. This yielded 43,969 total unique probes to 11,506 clusters, with a mean of 2.6 probes per cluster. To help control for the effects of interspecific sequence variation on probe performance, the above probes were compared to M. galloprovincialis clusters using BLAST. Probes designed to the M. californianus library that successfully aligned with the smaller M. galloprovincialis library had counterparts designed using the M. galloprovincialis sequence. This resulted in 556 matched pairs of probes, with a mean number of 4.6 mismatches per probe. Altogether, there were 44,524 unique probes that were duplicated or triplicated randomly to fill a 105k-feature microarray and in-situ synthesized by Agilent Technologies, Inc. (Santa Clara, CA, USA).


title: Agilent_Dm_5.1_1M_tiling

status: Public on Nov 04 2010

city: Durham

first: David

last: MacAlpine

state: NC

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

organism: Drosophila melanogaster

description: high resolution tiling array for modENCODE. Average probe spacing of 117 bp for Drosophila genome (5.1) and unique heterochromatin scaffolds.

first: Jared

last: Nordman

first: Joseph

last: Prinz

manufacture_protocol: Agilent Technologies


title: RIKEN BRC Human 11k Microarray Platform for Sense-Antisense Transcripts

first: Rintaro

last: Saito

first: Keisuke

last: Kohno

first: Yuki

last: Okada

first: Yuko

last: Osada

first: Koji

last: Numata

first: Chihiro

last: Kohama

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Akio

last: Kanai


title: Streptococcus pneumoniae TIGR4 4 x 2K

city: Bronx

first: Masahide

last: Yano

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

organism: Streptococcus pneumoniae TIGR4


title: [hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [exon-level]

status: Public on Jan 27 2011

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

description: Inflammation and the Host Response to Injury Program

first: Wenzhong

last: Xiao

first: Ronald

last: Davis

last: Tompkins

manufacture_protocol: See Manufacturers website


title: [scrGLYCO-v1F] Custom Affymetrix Glyco v1 GeneChip

status: Public on Oct 23 2010

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

organism:
Homo sapiens
Mus musculus

description:
The Glyco v1 array was designed in 2001 and consists of 3' probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from either species.

Most of the human probe sets on the Glyco v1 array were taken directly from the commercial U133A,B human array although a substantial number of the probesets were custom designed by Affymetrix from accessions for genes not well represented by the U133A,B. At the time, the Mouse 430 array had not yet been released by Affymetrix so mouse probesets were all custom designed by Affymetrix for this array  using the U133A,B design algorithms. In most cases, probesets consist of 11 probe pairs designed using the Perfect Match/Mismatch approach developed by Affymetrix.

manufacture_protocol: see manufacturer's web site


title: miRXplore TM Microarray (922)

status: Public on Oct 05 2010

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 6228 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1460 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1460 miRNA sequences covered sequence verified miRNAs of the species human (878) mouse (696) and rat (426) as well as viral miRNAs (141) and further mammalian species (76) as deposited in the miRBase sequence database version 10.1. 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: Exiqon miRCURY LNA microRNA array v.8.1

status: Public on Aug 12 2010

city: Boston

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

organism: Rattus norvegicus

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


title: MYcroarray CUSTOM Ecoli-str:K12-substr:MG1655 80K-6rep v1.0

status: Public on Aug 09 2010

city: Ann Arbor

first: Donald

last: Schwartz

state: MI

address: 5692 Plymouth Road

institute: MYcroarray

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

description: Circular features are ~55um in diameter.  4,280 E. coli genes are surveyed. The number of unique probe sequences per gene is either three (n = 3723), two (n =352) or one (n = 205). Consequently, there are 12,078 unique probe sequences surveying E. coli genes on the array. All probe sequences are replicated 6 times, so there are 72,468 E. coli probes on the array. In addition, there are 1,440 proprietary QC probe sequences on the array, 224 are for assessing hybridization efficiency. 8,012 potential feature locations contain no probe sequence.

first: Jean-Marie

last: Rouillard

manufacture_protocol: Oligonucleotides are synthesized directly on glass slides using standard phosphoramidite chemistry. Photo-lithography, driven by micro-mirror technology, is used to control the precise location of photo-generated acid production from an acid precursor. The acid removes a protection group (which prevents monomer oligomerization) on the terminal monomer. Only the deprotected spots can react with a new monomer. Uniquely, MYcroarray’s proprietary technology allows synthesis in liquid phase without physical barriers, masks or ink jets.


title: [Cytogenetics_Array] Affymetrix Cytogenetics Whole-Genome 2.7M Array

status: Public on Nov 03 2010

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

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

#%chip_type=Cytogenetics_Array
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00
#%dbsnp-date=2010-04-00
#%dbsnp-version=131
#%dgv-date=2010-03-00
#%dgv-version=9
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%netaffx-annotation-date=2010-07-00
#%netaffx-annotation-netaffx-build=31


title: Salmonella typhimurium/typhi version 5

status: Public on Nov 11 2009

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description:
This is a condensed template of quadruplicated features of PFGRC/JCVI Salmonella typhimurium/typhi version 5 microarray.
For full template information please refer : http://pfgrc.jcvi.org/index.php/microarray/array_description/salmonella_typhimurium/version5.html
The GAL Annotation File is linked as a Supplementary file at the foot of the record.

manufacture_protocol: Microarray Version - 5; Number of Grids - 48; Element Type - 70mer Oligonucleotide; Surface Coating – Aminosilane; Oligonucleotides Designed -5462; Replicate Oligo Printings - 4x; Controls - 500 Arabidopsis thaliana 70mers; 10 Arabidopsis thaliana amplicons.


title: NCI-Duke human chr06q27 385k 4bp-average-spacing 60mers

status: Public on Oct 04 2009

first: Michael

last: Kelley

address: 508 Fulton St. (111G)

institute: Duke University

manufacture_protocol: 385K element tiling array of a 2 MB region on chr6q27 (sequence based on NCBI Build 36 of the human genome HG18); 60-mer tiling with a median probe spacing of 4 bp. The NimbleGen design files (080905_HG18_RY_CGH.pos and 080905_HG18_RY_CGH.ndf) are included as supplementary files


title: μRNA spotted oligo array version 17.0 microRNA 1461 features human mouse rat chicken viral

status: Public on May 12 2010

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

institute: University of Oxford

organism:
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: spotted oligos, dimeric sequences linked to amine linker


title: MRC Homo sapiens 6.06K

status: Public on Sep 01 2008

city: Leicester

first: Timothy

middle: William

last: Gant

address: Hodgkin Building, University of Leicester

department: Systems Toxicology

institute: Medical Research Council Toxicology Unit

manufacturer: Systems Toxicology Group. Medical Research Council

first: Katie

last: Ridd

manufacture_protocol: Spotted cDNA array utilising IMAGE EST clones on poly-L-lysine. Spotted using a spotter of the Stanford design. Labelling is indirect two color using Alexa dyes. Full details and downloads available at www.systems-toxicology.com


title: Agilent-UNC-custom-4X44K

status: Public on Aug 05 2010

city: Chapel Hill

first: Matthew

middle: D

last: Wilkerson

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Agilent number 015102

manufacture_protocol: Agilent printing protocol


title: Human 387K miRNA Nucleosome Tiling Array HG18 Build 36 V1.0

status: Public on Nov 16 2008

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: Nucleosome mapping in 20 kb upstream regions of microRNAs.  Chromosome coordinates are based on the Build 36 HG18, March 2006 release.

first: David

last: Fisher


title: Invitrogen ProtoArray v4 human protein microarray lot HA20085

status: Public on Sep 01 2009

city: Rotterdam

first: Guido

last: Jenster

department: Urology

institute: Erasmus MC

first: Flip

last: Jansen

first: Angelique

last: van Rijswijk

first: Wilma

last: Teubel

manufacture_protocol:
The ProtoArray® Human Protein Microarray is a high-density protein microarray containing approx. 8000 purified human proteins. Each human open reading frame (ORF) is expressed as an N-terminal GST fusion protein using a baculovirus expression system, purified from insect cells, and printed in duplicate on a nitrocellulose-coated glass slide. The human proteins spotted on the microarray are expressed in insect cells using an optimized process to maximize the production of soluble recombinant proteins.
http://www.invitrogen.com/protoarray


title: EJH Mcat Oligo-DNA Microarray 3

status: Public on Oct 28 2008

city: Dallas

first: Eric

last: Hansen

state: TX

address: 5323 Harry Hines Boulevard

department: Microbiology

institute: University of Texas Southwestern Medical Center

organism: Moraxella catarrhalis

first: Wei

last: Wang

manufacture_protocol: The oligonucleotides were synthesized by Qiagen and spotted in triplicate on Corning UltraGapII slides


title: Largemouth Bass oligo array

status: Public on Aug 01 2008

city: Ocean SPrings

first: Joe

last: Griffitt

state: MS

address: 703 East BEach Drive

department: Coastal Sciences

institute: University of Southern Mississippi

organism: Micropterus salmoides

first: Natalia

last: Garcia-Reyero

first: Robert

first: Li

last: Liu

first: Kevin

last: Kroll

first: William

middle: G

last: Farmerie

last: Barber

first: Nancy

last: Denslow

manufacture_protocol: A normalized cDNA library was constructed and sequenced (454 pyrosequencing) using a GS20 pyrosequencer. Agilent's E-Array service was used to construct a microarray from this information.


title: USP Schistosoma mansoni 44K oligo array version 1.0

status: Public on Dec 20 2007

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

organism: Schistosoma mansoni

first: Sergio

last: Verjovski-Almeida

first: Thiago

last: Venancio

first: Giulliana

middle: T

last: Almeida

first: Ricardo

last: DeMarco

manufacture_protocol: All transcript information for S. mansoni available at both nr and dbEST databases at GenBank as of March, 2006 were filtered for contaminants and assembled with the CAP3 program. BLASTx were performed against the nr, with a cutoff of 1x10-10. The highest score alignment was used for annotation and assignment of the coding strand, in which the probe was designed. Those without significant hits against nr were annotated as no match, and probes for both strands were designed. In order to include possible new S. mansoni genes that have orthologous expressed sequences in S. japonicum but have not yet been cloned and sequenced in S. mansoni, we adopted the following strategy: S. japonicum RNA sequences from GenBank were assembled and submitted to a tBLASTx search against our assembled S. mansoni sequence set, and those with e-value lower than 1x10-20 were discarded. The remaining sequences were considered as S. japonicum transcripts without a clear corresponding S. mansoni transcript in the public database, thus being a candidate for a new S. mansoni gene. In order to obtain the S. mansoni sequence corresponding to these transcripts, the S. japonicum sequences were submitted to a BLASTn search against the S. manoni genome assembly (version 3), downloaded from the Wellcome Trust Sanger Institute. S. mansoni genomic loci that produced an alignment with at least 100 bases and had an identity higher than 70% were selected. Alternatively, tBLASTx was used, and S. mansoni genomic sequences were selected when they matched at least two high-scoring segment pairs (HSPs) each with e-value below 0.005. These conserved regions in the S. mansoni genome  were subsequently used in the probe design process. For each contig or singlet from the assembly, we selected all 60-mer sequences that satisfied a series of conditions that have been established by Agilent Technologies as follows: probes should not have 8 or more bases derived from low complexity regions; they should have a GC content of 35-55% and a melting temperature (Tm) of 68-76 Celsius degrees. In order to reduce cross-hybridization, each 60-mer sequence was searched by BLASTn against the S. mansoni genome sequence, downloaded from the Wellcome Trust Sanger Institute. In case that no hits were produced in this first search, the probes were used in a BLAST search against the CAP3 assembled mRNA/EST sequences. Probes were selected that had 100% match to the target sequence, which translates into a best-match alignment bit-score of 119. Those selected 60-mer sequences were checked for a low probability of cross-hybridization to non-specific targets by selecting probes for which the alignment bit-score of the second-best match  was equal to or lower than 42.1. The selected probes were carried forward to the last step, which consisted of picking the probe closest to the 3-end for eachh target.


title: MBPL human 30k P6

status: Public on Jun 04 2008

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: There are 32448 spots within a array.7334 human clone were printing 4 duplicate in a array. Additionally, we printing 10 doping control genes (SpotReport™-10 Array Validation System , Stratagene) and one house-keeping gene , 5 negative control gene as quality control indicator. total 16 quality control indicator were printing 2 duplicate in each block.

first: Ian

middle: C

last: Hsu

first: MinLung

last: Tsai

first: HuaKuo

last: Lin

first: WeiChung

last: Cheng

first: ChingLung

last: Huang

first: ChiuTing

first: YuLing

last: Hsieh

first: KunYu

first: TsaiJiuan

last: Weng

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 25~27°C and Humidity about 49~51%, and printing on April 2005. cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3×saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS Ⅱ coated slides (Corning Incorporated)coating of pure gamma amino propylsilane.


title: UMMS Drosophila melanogaster 454 sequenced small RNAs

status: Public on Jan 21 2008

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

technology: other

description: The "expected miRNA* extremities" are the extremities described in miRBase ( http://microrna.sanger.ac.uk/sequences/ ) for the few miRNA*s which have been experimentally validated; for the others, the miRNA sequence (as annotated in miRBAse) was used to infer the sequence of the corresponding miRNA* (this is called "conceptual dicing"). All these annotations were based on the latest release of miRBase (release 10.0, August 2007).

first: Megha

last: Ghildiyal

first: Phillip

last: Zamore

manufacture_protocol: (not applicable)


title: Schistosoma mansoni microarray v1

status: Public on Aug 24 2006

first: Katia

manufacturer: Instituto de Quimica - Universidade de Sao Paulo (IQ-USP)

middle: M

first: Sergio

manufacture_protocol:
We have constructed a 9,216-element microarray (4,608 unique elements in duplicate) using EST clones from a large scale sequencing of the S. mansoni transcriptome [Verjovski-Almeida et al., Nature Genet. 35:148-157, 2003]. We used the assembly of S. mansoni ESTs produced by this large-scale project (available at http://bioinfo.iq.usp.br/schisto/) for data mining and selection of relevant transcripts to be spotted. After sorting out the transcripts of interest (see below), we selected for each transcript the 3'-most clone from its cluster. These clones were amplified using PCR in combination with universal primers designed from the cloning site vector sequences flanking the inserts.  PCR products were purified using MultiScreen PCR 96 filter plate (Millipore), following manufacturer instructions. Successful amplification and purification of products were verified by agarose gel electrophoresis stained with ethidium bromide. Purified products eluted in 50 mM phosphate buffer pH 8.0 were spotted on Type 7-star glass slides (GE Healthcare), using a Generation III Microarray System (GE Healthcare).  A non-redundant set of 4,088 probes representing different SmAEs [Verjovski-Almeida et al., Nature Genet. 35:148-157, 2003] plus positive and negative controls was selected for array construction, using both manual and automatic methods.  We selected and mannually curated 1,104 probes, each one representing a gene with a biological function of interest as determined by comparing the translated S. mansoni EST contig sequences (using the BLASTx tool and a cutoff E-value of e-10) to the GenBank protein database and the Gene Ontology (GO) annotation bank. Among these, there are probes representing 290 genes involved in protein and amino acid metabolism, 50 in carbohydrate metabolism, 5 in RNAi, 20 in iron metabolism, 10 in purine and pyrimidine metabolism, 40 in lipid metabolism, 50 in DNA repair, 70 in transporters, 45 in cellular adhesion, 15 in apoptosis, 70 in cell cycle, 30 in protein processing and 150 in signaling processes and receptors. We also selected 696 probes automatically from genes coding for S. mansoni orthologs (among them 241 annotated as hypothetical or unknown). Selection criteria were: 1) a BLASTx search in GenBank (cutoff E-value e-10) shows that they match to proteins of other organisms; 2) no GO terms associated; 3) the sequence comes from a SmAE contig (not a singlet); 4) best hit must not be a bacterial protein. In addition, there are 1,155 probes for Schistosoma gene transcripts with the highest protein-coding scores as determined by ESTscan but no-match by BLASTx search against GenBank, which probably code for proteins of yet unknown function, and 1,133 probes for Schistosoma genes without protein-coding potential and no-match by BLASTx search against GenBank. The last line of each of 12 subarrays contained a set of Lucidea Universal scorecard controls (GE Healthcare), which include 2 negative controls per set, totalizing 48 negative control spots per slide that were used as a cutoff value for filtering out low intensity gene signals. Each probe in the array is spotted in duplicate, at the left and right halves of the slide, totalizing 9,216 spots per slide.
=============================================================================
=======================ANNOTATION UPDATE - May 2007 ===============================
We have updated the automatic annotation of our platform.  The controls (424) and manually curated genes annotations remain unaltered (1143 genes). The automatic selected genes are now categorized on: automatically selected with functions (656), automatically selected with no function (hypothetical) (867). The unkown genes are categorized on: Unknown coding (645) and unknown non coding (873), based on ESTscan results.


title: YALE/NIMBLEGEN HUMAN-CHR11-beta-globin-locus 3K v1.0

status: Public on Feb 16 2006

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

first: Alexander

last: Urban

middle: O

first: Rebecca

last: Selzer

first: Todd

last: Richmond

first: Joseph

middle: F

last: Cubells

first: April

last: Hacker

first: George

middle: V

last: Popescu

first: Roland

last: Green

first: Beverly

last: Emanuel

first: Mark

last: Gerstein

first: Sherman

last: Weissman

first: Michael

last: Snyder

manufacture_protocol:
Maskless array synthesis [1] was used to construct isothermal arrays, This array contains oligonucleotides that start every 9 bp on average and tiles the beta-globin locus on chromosome 11 (human genome build NCBI35/hg17 was utilized). The oligonucleotides were designed to be of variable length, adjusted to match a target melting temperature of 76°C according to the following formula: Tm = 81.5 + 16.6*(log10([Na+])) + 0.41*(%GC) - 600/length. Probe lengths were constrained to be a minimum of 45 bp and maximum of 85 bp.

[1] Nuwaysir, E.F., Huang, W., Albert, T. J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J. P., Ballin, J. et al., Genome Res., 2002. 12: p. 1749-1755, PMID: 12421762, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12421762


title: Adelaide Microarray Facility CompuGen Human 19K Oligo Library

status: Public on Jun 16 2007

city: Adelaide

first: Blair

last: Hopwood

state: South Australia

address: Frome Road

department: Tissue Pathology

country: Australia

institute: Institute of Medical and Veterinary Science

manufacture_protocol: See www.microarray.adelaide.edu.au for printing details.


title: YALE/NIMBLEGEN HUMAN-CHR11-beta-globin-locus 6K v1.0

country: USA

middle: E

middle: B

manufacture_protocol:
Maskless array synthesis [1] was used to construct isothermal arrays tiling the 100kb beta globin locus. This array contains overlapping oligonucleotides that start every 9 bp and tiles the entire nonrepetitive part of human chromosome 11 (human genome build NCBI34/hg16 was utilized).  Repetitive elements were identified using RepeatMasker [2] and oligonucleotide probes were designed to
represent the nonrepetitive DNA sequence. The oligonucleotides were designed to be of variable length, adjusted to match a target melting temperature of 76C according to the following formula: Tm = 81.5 + 16.6*(log10([Na+])) + 0.41*(%GC) - 600/length. Probe lengths were constrained to be a minimum of 45 bp and maximum of 85 bp.

[1] Nuwaysir, E.F., Huang, W., Albert, T. J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J. P., Ballin, J. et al., Genome Res., 2002. 12: p. 1749-1755, PMID: 12421762, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12421762

[2] Smit, A.F.A., Hubley, R. & Green, P., RepeatMasker Open-3.0, 1996-2004.


title: Illumina GoldenGate Methylation Cancer Panel I

status: Public on Sep 11 2009

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.