title: IGB_mouse_+33k_McC14

status: Public on Jan 31 2014

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

organism: Mus musculus

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Institute for Genomics and Bioinformatics, Graz University of Technology

manufacture_protocol: See publications: Hackl et al., Genome Biology,2005; Prokesch et al., Nucleic acid research, 2011; Pinent M et al., Genomics, 2008; Details:The mouse cDNA array platform containing 33184 spots was produced in-house. PCR amplification of several cDNA libraries (see(Hackl et al., 2005))  using universal primers (M13 Forward: 5’-GTT TTC CCA GTC ACG ACG TTG-3’, M13 Reverse: 5’-GAG CGG ATA ACA ATT TCA CAC AG-3’, end concentration: each 0.2 µM) was performed with a PTC 225 Tetrad (MJ Research) thermal cycler. The reaction volume of 100 µl contained 1x reaction buffer, 0.04 U/µl HotfirePol DNA Polymerase, 2mM MgCl2 (all from Solis Biodyne), dNTP mix (0.25mM each, Peqlab), primers and 2 µl template. After activation of the polymerase (95°C, 15 min) the program (95°C for 1 min, 62°C [decreasing to 52°C within the first 20 cycles] for 45 sec, 72°C for 2 min) was cycled 30 times, followed by a final elongation phase (72°C, 15 min). Products were visualized on 1.5% agarose gels (24x24 cm) with ethidium bromide. Plates with a low performance (high number of double bands or missing bands) were repeated. Unpurified PCR products were spotted in 3xSSC, 1.5M Betaine with a Microgrid 2 robot (Biorobotics) on epoxy silane slides (Schott) under stringent atmospheric conditions (21°C ± 1 and relative humidity 50% ± 5).


title: Illumina Genome Analyzer IIx (Arabis alpina)

status: Public on Jan 30 2014

last: GEO

country: USA

organism: Arabis alpina

technology: high-throughput sequencing

distribution: virtual


title: [MedGene-1_0] Affymetrix Medicago Gene 1.0 ST Array [probe set (exon) version]

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Medicago

technology: in situ oligonucleotide

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=MedGene-1_0-st
#%lib_set_name=MedGene-1_0-st
#%lib_set_version=1.0
#%create_date=Thu Apr 18 15:17:04 PDT 2013
#%pgf_format_version=1.0
#%probesets=108905

distribution: commercial

manufacture_protocol: See manufacturer's web site


title: Agilent-025355 Danio rerio ZV8400K

status: Public on Jan 29 2014

city: Charlestown

first: David

last: Langenau

state: MA

institute: Massachusetts General Hospital

organism: Danio rerio

description:
ZV8 array

Arrays of this design have barcodes that begin with 16025355 or 2525355.

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.

distribution: custom-commercial

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


title: Illumina HiSeq 2000 (Rosa chinensis)

status: Public on Jan 28 2014

organism: Rosa chinensis


title: Invitrogen NCode Human Non-coding RNA Microarray (NCRAH-02)

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

country: Germany

institute: Max Planck Institute for Infection Biology

organism: Homo sapiens

technology: spotted oligonucleotide

description:
Based on hg18; NCBI36; Mar2006
NCode_Human_ncRNA_v1_021441_ncRNA_v1_human

manufacture_protocol: See manufacturer's website.


title: Illumina HumanHT-12_V3_0_R1_Bioconductor_2.11

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

technology: oligonucleotide beads


title: Agilent-019647 Kogan-custom-mouse1 014868 array (Probe Name version)

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
Kogan custom mouse array v1
Arrays of this design have barcodes that begin with 16019647 or 2519647.
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: Escherichia coli O157:H7 4*72K

city: Hangzhou

first: Cai

last: Haiying

address: #866 Yuhangtang Road

country: China

institute: Zhejiang Universtiy

organism: Escherichia coli

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Drechslerella stenobrocha)

status: Public on Jan 27 2014

organism: Drechslerella stenobrocha


title: Agilent-037305 SurePrint G3 Human Custom CGH Microarray 4x180K

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description:
Arrays of this design have barcodes that begin with 16037305 or 2537305.
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: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: htmg430pmmmentrezgaltrabio131580]

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

country: France

institute: CIRI, centre international de recherche en infectiologie

description:
The CDF was further customized from the one provided by BrainArray:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/entrezg.download/htmg430pmmmentrezgcdf_17.1.0.tar.gz)

relation: Alternative to: GPL11180 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Sinorhizobium fredii NGR234)

status: Public on Jan 24 2014

organism: Sinorhizobium fredii NGR234


title: AB TaqMan Array Human microRNA A/B Cards v2.0 comp

status: Public on Dec 07 2014

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

technology: RT-PCR

description:
catalog number 4400238
miRNA PCR assay cards
Applied Biosystems Taqman miRNA PCR assay low density cards A and B including 671 non-redundant assays


title: Agilent-023673 ECSFRI medaka 4x44K

city: Shanghai

first: Zongli

last: Yao

address: No.300 Jungong Road

institute: East China Sea Fisheries Research Institute

organism: Oryzias latipes

manufacture_protocol: Aglient Custom Gene Expression Microarray, 4x44K. Catalog # G2514F. Manufacturer's web site at http://www.agilent.com/


title: Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840

status: Public on Jul 17 2014

city: Washington

first: Jeffrey

last: Bethony

state: DC

address: 2300 Eye St. NW.

department: Microbiology, Immunology, and Tropical Medicine

institute: George Washington University


title: L. monocytogenes EGDe array

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

organism: Listeria monocytogenes EGD-e

manufacturer: 70mer oligodeoxyribonucleotides, covering all 2857 open reading frames of the L. monocytogenes EGDe, were ordered from Operon Biotechnologies (Cologne, Germany). Oligos were spotted on the slides by BioCat GmbH (Heidelberg, Germany).

manufacture_protocol: Oligos are spotted in duplicate on epoxy-coated glass slides.


title: Illumina HiSeq 2000 (Hepatitis A virus; Homo sapiens)

status: Public on Jan 23 2014

organism:
Homo sapiens
Hepatovirus A


title: Illumina HiSeq 2000 (Tragopogon dubius)

organism: Tragopogon dubius


title: NimbleGen_Sphingomonas. sp A1 Array [2009-03-06_RDKK176_SPhi_60mer_expr]

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

organism: Sphingomonas sp. A1

description: NimbleGen design name 2009-03-06_RDKK176_SPhi_60mer_expr, NimbleGen design ID 9298. Type of array: Prokaryotic Expression (4plex); Number of target: 3,988; Length of probes: 60 mer; Number of probes per target: 9 pair; Density: 1 in 2; Replicate: 2; Total number of probes: 71,292.

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


title: Agilent-015241 Rice Gene Expression 4x44K Microarray (Probe name version)

status: Public on Jul 16 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Oryza sativa

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL6864.


title: [HG-U133_Plus_2] GeneNet Human 50K lentiviral shRNA Library

city: Leipzig

first: Manfred

last: Kunz

address: Philipp-Rosenthal-Str. 23

department: Department of Dermatology

institute: University of Leipzig

description:
Description of annotation procedure and files
=============================================

In this study, the Affymetrix HGU133 Plus 2 array [HG-U133_Plus_2] was not used in a standard gene expression experiment but in a shRNA screen.

The GeneNet Human 50K lentiviral shRNA Library uses several probes of the array to measure the abundance of specific shRNAs targeting the corresponding gene. However, in contrast to a gene expression study, probes for the same gene belong to different shRNAs and should therefore be analyzed separately and not summarized. Therefore, annotation information was extracted from several sources given below and used to annotate individual shRNAs after preprocessing using MAS for background correction and RMA for normalization.

- H50_no_x_lib.dat
File from GeneNet H50K software (version 3.2) giving information (e.g. sequences) of probes used for shRNA screening

- HGU133Plus2_Hs_ENST.cdf
custom CDF version 12.1 for Ensembl transcripts (see http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v12) used to map probes to transcripts

- infos_probes_single_siRNA_probes_with_names.txt
information about siRNAs which sequence match only a single probe:
sequence of siRNA, probe, location of probe on the array, mapping to Affymetrix CDF (hgu133plus2cdf_2.4.0 and hgu133plus2probe_2.4.0 Bioconductor packages), mapping to custom CDF (ENST, version 12)

- infos_probes_multiple_siRNA_probes_with_names.txt
information about siRNAs which sequence match to several probes (or several copies of probe sequence on array):
sequence of siRNA, probe, location of probe on the array, mapping to Affymetrix CDF (hgu133plus2cdf_2.4.0 and hgu133plus2probe_2.4.0 Bioconductor packages), mapping to custom CDF (ENST, version 12)

- infos_probes_background_probes_with_names.txt
information about probe sequences not used for shRNA screening were used to estimate background intensities


title: Illumina HiSeq 2000 (Tanacetum parthenium)

organism: Tanacetum parthenium


title: Mycobacterial 4100 oligo array (Operon Technologies)

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

organism: Mycobacterium tuberculosis

manufacturer: Johns Hopkins University microarray core facility

manufacture_protocol:
1.Oligos are arrayed in 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in water to 20 µM and rearray 5 µL into 384-well, polystyrene V-bottom plates.
3. Allow oligos to dry through passive water evaporation in a chemical hood.
4. Before printing, add 5 µL of 3X SSC to each well. This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Centrifuge plates at 500 rpm for 5 minutes.
9. 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.
10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
11. After the print run is completed, allow plates to dry through passive evaporation in a chemical hood.
12. For each subsequent preparation of these plates for a print run, add water to the wells instead of SSC. 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 printing run.


title: Agilent-021600 Custom Soybean Microarray (44K)

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

organism: Glycine max

manufacture_protocol:
The soybean microarray was designed using the server-based eArray platform (http://earray.chem.agilent.com/earray/) from Agilent Technologies (Wolber et al., 2006). The current slide layout consists of four arrays of >44,000 features, including a set of Agilent's positive and negative control features.
An oligonucleotide microarray containing 42,564 unique probes (60-mer) was created from 33,574 unigenes from Glycine max database (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3847) (May 2009) as templates for probe design.


title: SABiosciences Qiagen Human Adipogenesis RT² Profiler PCR Array PAHS049Z

city: roma

first: antonella

last: minutolo

address: viale del policlinico

description: PCR assay


title: Illumina HiSeq 2000 (Flaveria vaginata)

last: GEO

organism: Flaveria vaginata


title: Illumina HiSeq 2000 (Flaveria pubescens)

organism: Flaveria pubescens


title: Illumina HiSeq 2000 (Amphimedon queenslandica)

organism: Amphimedon queenslandica


title: Illumina HiSeq 2000 (Flaveria sonorensis)

organism: Flaveria sonorensis


title: Illumina HiSeq 2000 (Helenium autumnale)

organism: Helenium autumnale


title: Illumina HiSeq 2000 (Flaveria trinervia)

organism: Flaveria trinervia


title: Illumina HiSeq 2000 (Flaveria pringlei)

organism: Flaveria pringlei


title: Illumina HiSeq 2000 (Flaveria palmeri)

organism: Flaveria palmeri


title: Illumina HiSeq 2000 (Flaveria bidentis)

organism: Flaveria bidentis


title: Infinium HumanOmniExpressExome BeadChip

status: Public on Apr 01 2014

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

organism: Homo sapiens

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Flaveria cronquistii)

organism: Flaveria cronquistii


title: Illumina HiSeq 2000 (Flaveria brownii)

organism: Flaveria brownii


title: Illumina HiSeq 2000 (Ammopiptanthus mongolicus)

status: Public on Jan 21 2014

organism: Ammopiptanthus mongolicus


title: Illumina HiSeq 2000 (Flaveria angustifolia)

organism: Flaveria angustifolia


title: Illumina HiSeq 2000 (Flaveria kochiana)

organism: Flaveria kochiana


title: Illumina Genome Analyzer (Populus cathayana)

status: Public on Jan 17 2014

organism: Populus cathayana


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version, ENSG 60]

status: Public on Jan 19 2014

city: Cold Spring Harbor

first: Mads

middle: A

last: Jensen

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

organism: Mus musculus

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: Identical to GPL6246 but gene annotations are based on Ensembl version 60 (Nov 2010).


title: Illumina Genome Analyzer (Schizosaccharomyces pombe 972h-)

organism: Schizosaccharomyces pombe 972h-


title: NimbleGen Cavia porcellus 13K

city: Matsumoto

first: Shin-ya

last: Nishio

state: Nagano

address: 3-1-1 Asahi

department: Department of Otorhinolaryngology

institute: Shinshu University School of Medicine

organism: Cavia porcellus


title: Agilent-036667 Sinorhizobium meliloti Smexpr1

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: Texas

address: 6000 Harry Hines Blvd, NA5.146, NA5.146

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

organism: Sinorhizobium meliloti

description:
S. meliloti expression array

Arrays of this design have barcodes that begin with 16036667 or 2536667.

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: Illumina Genome Analyzer IIx (Echinococcus granulosus)

status: Public on Jan 16 2014

organism: Echinococcus granulosus


title: AB SOLiD 4 System (Zea mays)

organism: Zea mays


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: HG-U133_plus2,TCGAmin5]

city: New York

first: Milan

middle: Girish

last: Chheda

state: NY

address: 408 E. 69th Street

department: Neurology

institute: Memorial Sloan-Kettering Cancer Center

description: CDF file (HG-U133_Plus_2) from The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/tcga/tcgaPlatformDesign.jsp)

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 12.1.0]

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

description: Probe set data extracted from custom CDF [Brainarray Version 12.1.0]

relation: Alternative to: GPL5175 (Alternative CDF [official])


title: Rat teratogenicity custom array

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

institute: Hannover Medical School

organism: Rattus norvegicus

manufacture_protocol: The cDNA array was prepared using defined 200- to 400-bp fragments of selected and sequence-verified cDNAs. These probes were generated by RT-PCR (Superscript II; Invitrogen, Groningen, The Netherlands), cloned into the pGEM-T vector (Promega, Mannheim, Germany) and spotted in duplicate on different positions on the array (Thum and Borlak, 2008). In brief, the inserts were amplified using vector-sequence-derived primers with the sense primer carrying a 5′-amino modification. Amplified inserts were purified (Qiaquick 96 PCR BioRobot Kit; Qiagen), checked on an agarose gel and diluted to a concentration of 100 ng/Xl. Two nanolitres of diluted probe was spotted by dispensing 20 drops of 100 pl each as duplicates on treated glass slides with a customised ink jet spotter. Probes were re-hydrated for 2 h in a humidified chamber and blocked. As a qualitative measurement for the validity of the data and to check for the uniformity of the hybridization process, the standard deviation of the two ratios for the respective gene was calculated.


title: NimbleGen gut microbiome array [091124_micro_BZ_EXP_HX12]

city: Beijing

first: Yongfei

last: Hu

address: NO.1 West Beichen Road, Chaoyang District

department: CAS key Laboratory of Pathogenic Microbiology and Immunology

institute: Institute of Microbiology, Chinese Academy of Sciences

organism: gut metagenome

description:
NimbleGen design name: 091124_micro_BZ_EXP_HX12,
NimbleGen design ID: 10987

An detection design for 2916 antibiotic resistance genes from ARDB with twelve 60-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC control probes.

The .ndf and .ngd files are linked below as supplementary files. However, please note that not all genes in the ngd file are represented in the platform data table. The Platform data table reflects a condensed representation of the array's replicate (SEQ_ID) features.

The 'rep*' appended to each identifer reflects the 'BLOCK' designation in the 'CONTAINER' column of the ndf file.  For example, *rep1 represents the probes with the 'BLOCK1' designation in the 'CONTAINER' column of the ndf file.

native array description file: 091124_Micro_BZ_EXP.ndf
native array description file: 091124_Micro_BZ_EXP.ngd


title: FPL/Cullen-Phanerochaete chrysosporium RP-78 microarrays v2.0 [090423_Phan_Chry_UW_DC_expr]

status: Public on Jan 15 2014

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

organism: Phanerochaete chrysosporium RP-78

description:
Standard NimbleGen synthesis of 60 mers. Twelve oligos for each of 9959 genes

designname: 090423_Phan_Chry_UW_DC_expr
designid: 9865

The .ndf file is linked below as a supplementary file.

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


title: Custom oligonucleotide CGH Microarray 4x44K  designed by Genotypic Technology Private Limited (AMADID: 20515)

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center


title: MASK design peptide microarray

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

organism: synthetic construct

technology: spotted peptide or protein

manufacturer: Peptide Array Core at Arizona State University

manufacture_protocol:
Non-contact Piezo printing (by Applied Microarrays, Tempe, AZ) onto Schott Nexterion A+ aminosilane slides using maleimide conjugation to the free sulfur on the cysteine of the NH3-terminus of peptides
Pre-synthesized 17mers


title: Illumina MiSeq (Capsicum annuum)

organism: Capsicum annuum


title: Agilent-034889 Bacillus anthracis array (condensed version)

city: New Delhi

first: Gurudutta

last: Panda

address: New Mehrauli Road

department: School of Biotechnology

institute: Jawaharlal Nehru University

organism: Bacillus anthracis str. 'Ames Ancestor'

description:
NCBI Accession numbers:
gi|50196905|ref|NC_007530.2, gi|47566322|ref|NC_007322.2, and gi|50163691|ref|NC_007323.3

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


title: Illumina Genome Analyzer IIx (Trypanosoma cruzi)

organism: Trypanosoma cruzi


title: Ion Torrent PGM (Ovis aries)

status: Public on Jan 10 2014

organism: Ovis aries


title: Illumina HiSeq 2000 (Tetramorium bicarinatum)

organism: Tetramorium bicarinatum


title: Illumina HiSeq 2000 (Homo sapiens; Human immunodeficiency virus 1)

organism:
Homo sapiens
Human immunodeficiency virus 1


title: Agilent-025954 Streptomyces avermitilis Matriz_JFA_V1

city: Porto

first: Tiago

last: Beites

address: rua do campo alegre, 823

country: Portugal

institute: IBMC

organism: Streptomyces avermitilis

description:
S.avermitilis and polienos
Arrays of this design have barcodes that begin with 16025954 or 2525954.
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: Illumina HiSeq 2000 (Streptococcus pneumoniae)

organism: Streptococcus pneumoniae


title: Mouse alternative splice junctions array

status: Public on Jan 14 2014

last: Lazarev

address: 1212 Amsterdam Av

department: Biological Sciences

institute: Columbia University

organism: Mus musculus

first: Jian-Bing

last: Fan

first: Joanne

last: Yeakley

first: Marina

last: Bibikova

first: Eugene

last: Chudin

first: Eliza

last: Wickham

first: Jing

last: Chen

last: Doucet

first: Philippe

last: Rigault

first: Baohong

last: Zhang

first: Richard

last: Shen

first: Celeste

last: McBride

first: Hai-Ri

last: Li

first: Xiang-Dong

last: Fu

first: Arnold

last: Oliphant

first: David

last: Barker

first: Mark

last: Chee

manufacture_protocol: Zip code-containing oligos were spotted on a chip (the details are proprietary)


title: Institute for Environmental Genomics (IEG) GeoChip 4.2 [by Beijing University of Chemical Technology]

first: Xiaohui

last: Wang

address: 15 beisanhuan east road, chaoyang district, beijing, 100029

organism:
Bacteria
Archaea
Eukaryota
Viruses

manufacturer: Institute for Environmental Genomics (Norman, OK)

manufacture_protocol:
http://ieg.ou.edu/protocol.htm
Microbes in activated sludge


title: NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array [090618_MM9_CpG_Refseq_Prom_MeDIP]

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

description:
Format:3x720K
Source: UCSC
Build: Hg18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 2509bp

manufacture_protocol: See www.nimblegen.com


title: Agilent-031301 Mus musculus Issa methylation 11-16-10-JCJ

status: Public on Jan 09 2014

city: Smithville

first: Yue

last: Lu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
Arrays of this design have barcodes that begin with 16031301 or 2531301.

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: Illumina HiSeq 2500 (Tribolium castaneum)

status: Public on Jan 13 2014

last: GEO

organism: Tribolium castaneum


title: NimbleGen Clostridium thermocellum ATCC 27405 HX12 array (12 x 135k)(non-condensed version) [080724_C_thermo_27405_expr]

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

organism: Acetivibrio thermocellus ATCC 27405

description:
Custom array
Native array description file: 080724_C_thermo_27405_expr.ndf
Native array description file: 080724_C_thermo_27405_expr.ngd

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


title: Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description:
Human and human viral miRNAs

Arrays of this design have barcodes that begin with 16031181 or 2531181.

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.


title: Custom Human TLDA 64-Circulating tumor cell associated gene panel

city: San Francisco

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description:
We selected 64 genes from previously published data focused on QPCR analyses of CTCs. Included in the list are clinically relevant genes, stem cell and epithelial-mesenchymal transition (EMT) markers, and highly expressed genes in breast and prostate cancers. We also included EPCAM and PTPRC (encodes CD45) to measure the expression of these markers specific for epithelial cells and leukocytes, respectively. Also, included are 6 candidate reference genes for data normalization.
We designed a custom Taqman® Low Density Array (TLDA, Applied Biosystems) microfluidic card (384-well format) containing two sets of 64 Taqman® gene expression assays printed in triplicate.

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer IIx (Cunninghamia lanceolata)

organism: Cunninghamia lanceolata


title: Illumina HiSeq 1000 (Oncorhynchus mykiss)

status: Public on Jan 08 2014

organism: Oncorhynchus mykiss


title: NimbleGen Human Custom Array 4x72K [120202_Hsapiens_CV_exp]

status: Public on Jan 12 2014

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

institute: INSA


title: NimbleGen Mouse 385K RefSeq Promoter Array [2006-06-06_MM8_RefSeq_promoter]

city: Cambridge

first: Usue

last: Laresgoiti

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description: Based on mouse genome build mm8 (NCBI Build 36).

manufacture_protocol: See NimbleGen website (http://www.nimblegen.com/support/dna-microarray-support.html)


title: Illumina HiSeq 2000 (Saccharomyces cerevisiae W303)

status: Public on Jan 07 2014

organism: Saccharomyces cerevisiae W303


title: Agilent-031068 EmbryoGene Porcine Array V.1 (EMPV1; Probe Name version)

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

country: Canada

institute: University of Alberta

organism: Sus scrofa

description:
EmbryoGENE Porcine Embryo microarray
Custom Microarray GE 4x44K with designID=031068
Specific array desgin from porcine preimplantation development
Arrays of this design have barcodes that begin with 16031068 or 2531068.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL14925

first: Chi

last: Zhou


title: MGC cDNA screening array

city: Los Angeles

first: Meng

address: 2003 Zonal Avenue

institute: University of Southern California

organism:
Homo sapiens
Mus musculus

manufacturer: Scripps Cell Based Screening and Genomics core at the Scripps Research Institute's Florida

manufacture_protocol: The genome scale screen cDNA clone collection was the MGC Collection from Open Biosystems.  40 ng of each clone in the collection was plated in individual wells of a Greiner white bottom 384-well plate.


title: 110420_Ccre_JC_exp, 4plex array

city: Lausanne

first: Diego

last: Gonzalez

address: Quartier UNIL-Sorge, Bâtiment Biophore

department: Department of Fundamental Microbiology

institute: University of Lausanne

organism: Caulobacter vibrioides NA1000

description:
NimbleGen design name 110420_Ccre_JC_exp, NimbleGen design ID 416564. Each probe is replicated 3 times.  The design includes random GC and other control probes.
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.

first: Justine

last: Collier

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


title: Agilent-021506 Plasmodium falciparum UP1_01_Of_1

city: Pretoria

first: Shaun

last: Reeksting

state: Gauteng

address: Lunnon Rd.

department: Biochemistry

country: South Africa

institute: University of Pretoria

organism: Plasmodium falciparum

description:
Expression array of P.falciparum
Arrays of this design have barcodes that begin with 16021506 or 2521506.
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-026035 Scer_barcode_v2_200911

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

organism: Saccharomyces cerevisiae S288C

description:
Yeast KO collection barcode specific microarray, v2
Arrays of this design have barcodes that begin with 16026035 or 2526035.
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: NanoString nCounter Analysis System [Gorilla and Century CodeSets]

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 3

institute: Max Planck Research Unit for Neurogenetics

technology: other

manufacture_protocol:
http://www.nanostring.com/lifesciences/
Digital molecular barcoding technology


title: NimbleGen Drosophila Tiling 388k Array [2007-02-15_Dros_300bp_60mer]

status: Public on Jan 01 2014

first: francois

last: schweisguth

address: 25 rue du Dr Roux

organism: Drosophila melanogaster

description:
Release 4 genome from the Berkeley Drosophila Genome Project (BDGP).
Platform data table is based on the ndf file.

designname=2007-02-15_Dros_300bp_60mer
designid=5246

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


title: [hjay] Affymetrix GeneChip Human HJAY Array (gene array)

city: Rome

first: Maria Paola

last: Paronetto

address: Piazza Lauro de Bosis, 6

department: Department of Health Sciences

institute: University of Rome "Foro Italico"

manufacture_protocol: See manufacturers website


title: Prawn miRNA Array

city: hangzhou

first: Tianzhi

last: Huang

address: HANGZHOU

institute: ZJU

organism: Shrimp white spot syndrome virus

description: Part No.MRA-1001B1C


title: [BovGene-1_0-v1] Bovine Gene 1.0 Array [transcript (gene) version]

city: Burlington

first: David

middle: E

last: Kerr

state: VT

address: 500 Main Street 205 Terrill Hall

department: Animal Science

institute: University of Vermont

organism: Bos taurus

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

manufacture_protocol: See manufacturer's web site


title: Agilent-022702 Candida utilis Custom 8x15k Array

city: Yokohama-shi

first: Hideyuki

last: Tamakawa

state: Kanagawa

address: 1-13-5, Fukuura, Kanazawa-ku

department: Central Laboratories for Key Technologies

institute: KIRIN Co., Ltd.

organism: Cyberlindnera jadinii

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


title: Illumina HiSeq 2000 (Malus domestica)

status: Public on Jan 06 2014

last: GEO

organism: Malus domestica


title: Illumina Genome Analyzer IIx (Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130)

status: Public on Jan 04 2014


title: NimbleGen Mouse 3X720K [100727_GT_MM9_Ag_recep_ChIP]

status: Public on Jan 03 2014

first: Eugene

middle: M

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

organism: Mus musculus

description:
mm9

DESIGN_ID: 532181
designname: 100727_GT_MM9_Ag_recep_ChIP

native array description file: 100727_GT_MM9_Ag_recep_ChIP.ndf
native array description file: 100727_GT_MM9_Ag_recep_ChIP.pos

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


title: Agilent-040023 FZ_IBG1_4plex

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism:
Gluconobacter oxydans
Escherichia coli
Corynebacterium glutamicum
Bacillus subtilis subsp. subtilis str. 168

description: Based on Corynebacterium glutamicum (NC_006958), Bacillus subtilis str. 168 (NC_000964), Gluconobacter oxydans (NC_006677, NC_006672, NC_006673, NC_006674, NC_006675, NC_006676), Escherichia coli (NC_000913)

manufacturer: Agilent Technologies (Waldbronn, Germany)

manufacture_protocol: see Agilent Technologies


title: UofToronto-yeastORF-6.4k3.48

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

organism: Saccharomyces cerevisiae

manufacture_protocol: Double-spotted array containing 6,240 yeast ORFS (plus control spots totalling 6.4k)


title: Illumina HiSeq 2000 (Erwinia amylovora)

status: Public on Jan 02 2014

organism: Erwinia amylovora


title: Lactococcus lactis KF147 15K 60-mer array

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

organism: Lactococcus lactis


title: CodeLink Human Whole Genome Array [DISCOVERY probe type]

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

country: Spain

institute: University of Granada

organism: Homo sapiens


title: Agilent-032208 Aedes aegypti AgyptiLPSVer1 (Feature Number version)

city: Shinjukuku

first: Shinji

last: Kasai

state: Tokyo

address: 1-23-1 Toyama

department: Department of Medical Entomology

institute: National Institute of Infectious Diseases

organism: Aedes aegypti

description:
Arrays of this design have barcodes that begin with 16032208 or 2532208.

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: Agilent-023116 Human herpesvirus U75698

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

organism: Human herpesvirus 8 type M

description: The array contains probes for herpesvirus.

manufacture_protocol: Agilent Technologies


title: Agilent-032031 Pseudomonas_modified  (Probe Name version)

city: Lubbock

first: Uzma

last: Qaisar

institute: Texas Tech University

organism: Pseudomonas aeruginosa

description:
replicated probes added

Arrays of this design have barcodes that begin with 16032031 or 2532031.

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: [hjay] Affymetrix GeneChip Human HJAY Array (exon)


title: Agilent-029564 LBLGC-Ptrichocarpa (Probe Name version)

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

organism: Populus trichocarpa

description:
LBLGC-Ptrichocarpa

Arrays of this design have barcodes that begin with 16029564 or 2529564.

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: University of Minnesota - Streptomyces Microarray

city: Powai, Mumbai

first: Sarika

last: Mehra

state: MH

address: IIT Bombay

department: Chemical Engineering

institute: IIT Bombay

organism: Streptomyces coelicolor A3(2)

manufacturer: University of Minnesota - Chemical Engineering and Materials Science - Hu lab

manufacture_protocol: A whole genome cDNA microarray was constructed for S. coelicolor. Gene-specific probes with an average length of 500 bp were designed based on the genomic sequence database at Sanger Center to represent the 7,825 genes. The primers to amplify these probes were designed to be 20 bp in length with a melting temperature around 62 deg C. An iterative primer/probe design process was adopted. The primers were first Blasted against the entire genome to check for the specificity to the corresponding genes. The probe sequences resulting from these primers were also blasted against the entire genome to check for possible cross-hybridization with sequences other than the corresponding gene. Any primer pair that may give rise to a potentially croshybridizing probe sequence was redesigned with alternate coordinates. This probe checking-redesign process minimized the possibility of cross-hybridization between a probe and other cDNA species. For some highly homologous genes, a unique probe was not attainable and a multigene probe was used. A multigene probe was designed in such cases. 7,581 genes were successfully amplified and spotted on the microarray. The microarray was fabricated on poly-L-lysine slides with duplicate spots for each probe.


title: State Key Laboratory Human microRNA array 1888

city: Guangzhou

first: Heng-Ying

last: Pu

address: 651, Dongfeng East Road

institute: Cancer Centre, Sun Yat-sen University

manufacturer: State Key Laboratory of Oncology in South China,Sun Yat-sen University

manufacture_protocol: 1888 microRNA probes were printed onto slides using the SmartArrayerTM 136 printer (CapitalBio,Inc.,Beijing,China)


title: PIQOR Oncology Microarray

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

institute: CNRS UMR6290

manufacture_protocol: protocol according to Miltenyi Biotec


title: Exiqon Mouse miRCURY 6th generation LNA microRNA array

status: Public on Dec 31 2013

city: Austin

first: Giorgio

last: Gorini

address: 2500 Speedway A4800

department: Waggoner Center for Alcohol and Addiction Research

country: USA

institute: The University of Texas at Austin

description:
miRCURY 6th generation LNA™ microRNA array
microRNA Expression Profiling

first: Yury

middle: O

last: Nunez

first: Roy

middle: D

last: Mayfield


title: Nimblegen_Azospirillum lipoferum 4B_6.2 K

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

institute: Université de Lyon

organism: Azospirillum lipoferum 4B

description: no additional information

manufacture_protocol: The custom-array design was based on a 385K 4-plex Nimblegen array format and is composed of 4x62,178 probes. Array characteristics: Probe length = 60 bp, 5 probes per gene (mostly), 2 replicates per probe. Manufacturing and processing of arrays, hybridization and scanning were performed according Nimblegen's recommendations


title: IFC UNAM Mouse 22K v1

status: Public on Dec 21 2013

city: México DF

first: Reyna

last: Hernandez-Benitez

address: Circuito Exterior S/N Ciudad Universitaria

department: Neurociencias

country: Mexico

institute: Instituto de Fisiología Celular UNAM

manufacturer: Unidad de Microarreglos, IFC UNAM, México

first: Jorge

last: Ramírez

first: Lorena

middle: C

last: González

first: Simón

middle: G

last: León

first: José

middle: L

last: Torres

first: Gerardo

last: Coello

first: Gustavo

last: Corral

first: Ana

middle: P

last: Gómez

manufacture_protocol: The Mouse 65-mer oligo library from Sigma-Genosys oligo sets was used. It contains 22,000 gene specific oligonucleotide probes representing the 70% of mouse genome. Oligo library was resuspended to 50µM in Micro Spotting solution (ArrayIt Brand Products.). SuperAmine coated slides 25x75 mm (TeleChem International INC) were printed using SDDC robot (Virtek) with 48 pins (Y= 12 meta rows; X= 4 meta columns; Y1= 22 rows; X1= 22 columns; with a dot spacing of Y1= 190 micron and X1= 190 microns). Fixed at 80°C for 4 hours. For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C.


title: NimbleGen Mouse 3X720K

status: Public on Aug 14 2013

first: Eugene

last: Oltz

description:
mm9
native array description file: 100727_GT_MM9_Ag_recep_ChIP.ndf
native array description file: 100727_GT_MM9_Ag_recep_ChIP.pos


title: NimbleGen Human HG18 whole genome CGH 3x720K

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

description:
Annotation in this record based on NCBI human build 36.
whole genome, CGH with a median spacing of 2509 bp
native array description file : 100718_HG18_WG_CGH_v3.1_HX3.ndf
native array description file : 100718_HG18_WG_CGH_v3.1_HX3.pos


title: Capsicum annuum 300k Microarray v2.0

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

organism: Capsicum annuum

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf file is linked below as supplementary files.
071025_Sundow_pepper_expr.ndf
071025_Sundow_pepper_expr.ncd
Pepper_v2_SeqId_information_reference
Probes are designed from 29,580 unigenes and each unigene is featured by 10 probes.


title: Melitaea cinxia 4x44K v1.0 (Feature number version)

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

organism: Melitaea cinxia

description:
Normalized cDNA from genetically diverse pools of larvae, pupae, and adults body parts, across multiple local populations in the Åland islands were used to de novo assemble a partial transcriptome of the Glanville Fritillary butterfly using 454 pyrosequencing. Probes were designed using Agilent eArray based on the assembled contigs and singletons (version 1). In addition some Sanger sequences and known genes were included in the probe design. For most transcripts a single probe was printed on the array in triplicate. Some probes were also designed to detect possible SNP and splice variants.
Additional 454-pyrosequencing was conducted after the microarrays were designed. The new EST data was used to re-assemble and re-annotate the transcripts. The probes were matched to the new contigs and singletons (version 2) by BLASTn searches, which were then used to re-annotate the probes by BLASTx searches to other insect species.

Assembly sequences and additional information can be obtained from cinxiabase (http://cinxiabase.vmhost.psu.edu/)

first: Cristobal

last: Vera

first: Christopher

last: Wheat

first: Howard

last: Fescemyer

first: James

last: Marden

first: Douglas

last: Crawford

first: Mikko

last: Frilander

first: Ilkka

last: Hanski

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


title: LC Sciences MRA-1038 Plants miRNA Array (miRBase 16)

city: Hangzhou

first: Bo

last: Wang

state: zhejiang

address: Xiasha

country: China

institute: Zhejiang Sci-Tech University

organism: synthetic construct

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://microrna.sanger.ac.uk/sequences/) 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: Agilent-021825 3q7q_nov2008

city: Pierre Benite

first: Laurent

last: JALLADES

address: 165 Chemin du Grand Revoyet

country: France

institute: Hospices Civils de Lyon

description:
Arrays of this design have barcodes that begin with 16021825 or 2521825.

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.

A custom high-definition oligonucleotide microarray (4x44K, Agilent) was designed for aCGH from the online application tool eArray (version 5.3) and HD-CGH probe library (sequence source UCSC hg18 / NCBI Build 36). This custom microarray combines the capability to scan human genome-wide with an average resolution of approximately 100 Kb and to focus on regions of interest for highest resolution tiling (11 Kb-resolution for either chromosomes 3q and 7q). The array contains about 8,500 and 9,000 oligonucleotides spanning 97 Mb and 105 Mb of the 7q and the 3q chromosomes respectively.


title: Agilent-031068 EmbryoGene Porcine Array Version 1 (EMPV1)

status: Public on Jan 11 2012

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

organism: Sus scrofa

description:
EmbryoGENE Porcine Embryo microarray
Custom Microarray GE 4x44K with designID=031068
Specific array desgin from porcine preimplantation development
Arrays of this design have barcodes that begin with 16031068 or 2531068.

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.

A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL18148.

first: Stephen

last: Tsoi

first: Chi

last: Zhou


title: Arraystar human lncRNA microarray V1-100309 [gene-level version]

status: Public on Apr 05 2013

city: Rockville

first: Panos

last: Pan

state: MD

address: 9430 Key West Avenue

institute: Arraystar Inc.

description: This array contains ~19000 RefSeq coding genes and ~18000 long non-coding RNAs (lncRNA) and ~3000 lincRNAs.

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


title: NimbleGen Mus musculus 100205_MM8_Deluxe_Promoter_HX1 array

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description:
Platform annotations are based on build MM8
Platform column file lists unique non-control probes

DESIGN_ID: 11383
Design name: 100205_MM8_Deluxe_Promoter_HX1

native array description file: 100205_MM8_Deluxe_Promoter_HX1.pos
native array description file: 100205_MM8_Deluxe_Promoter_HX1.ndf

The GPL16157 and GPL16158 contain the same test probes but differ in control probes and placement of probes (i.e. the identical platform data tables).


title: NimbleGen Mus musculus 100718_MM8_Deluxe_Promoter_HX1 array

description:
Platform annotations are based on build MM8
Platform column file lists unique non-control probes

DESIGN_ID: 535413
Design name: 100718_MM8_Deluxe_Promoter_HX1

native array description file: 100718_MM8_Deluxe_Promoter_HX1.pos
native array description file: 100718_MM8_Deluxe_Promoter_HX1.ndf

The GPL16158 and GPL16157 contain the same test probes but differ in control probes and placement of probes (i.e. the identical platform data tables).


title: Custom Illumina GoldenGate DNA methylation Beadchip

status: Public on Sep 15 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

manufacture_protocol: See manufacturer's website


title: Agilent-022099 Custom Leuconostoc gasicomitatum LMG 18811 oligoarray 2.1

status: Public on Feb 07 2013

first: Elina

last: Jääskeläinen

address: P.O. Box 66 (Agnes Sjöbergin katu 2)

department: Food Hygiene and Environmental Health

institute: University of helsinki

organism: Leuconostoc gasicomitatum LMG 18811

manufacture_protocol: 8x15K microarrays. see manufacturer's web site at http://www.agilent.com/


title: Agilent-017910 pseudoobscura_v2

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

institute: Uppsala University

organism: Drosophila pseudoobscura

description:
D. pseudoobscura GLEAN predictions new design
Arrays of this design have barcodes that begin with 16017910 or 2517910.
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: Clostridium thermocellum ATCC 27405 9K (expr_HX12)

status: Public on Aug 16 2012

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Acetivibrio thermocellus ATCC 27405

description:
Custom array.
DESIGN_NAME: 080724_C_thermo_27405_expr_HX12

relation:
Alternative to: GPL15992
Alternative to: GPL18170


title: Lallemand Health Solutions Human Immune Array

status: Public on Dec 31 2011

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

institute: Lallemand Health Solutions Inc.

first: Julie

last: Audy

first: Timothy

last: Wallace

first: Olivier

last: Mathieu

manufacture_protocol: Genes were selected from the KEGG data base from specific pathways. Gene specific long oligonucleotides sequences (70-mers) were recovered from the Human Exonic Evidence Based Oligonucleotide (HEEBO) database. The oligonucleotides were synthesized (IDT integrated technology Inc. IA, USA) at a normalized concentration of 25 mM and spotted onto Corning UltraGAPS Coated Slides using a PBI robot from Virtex. The Immune Array design was repeated twice per slide in six subgrid and each gene was in duplicate. The microarray slides were printed at the NRC Biotechnology Research Institute (Montreal, QC Canada) in the Microarray Laboratory


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_15.0.0]

status: Public on Apr 22 2013

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HuGene10stv1_Hs_ENTREZG_15.0.0

relation: Alternative to: GPL6244 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: qChipPre BAC Version

city: BARCELONA

first: Lluis

last: Armengol

state: Catalonia

address: Doctor Aiguader, 88

institute: qGenomics

manufacture_protocol:
1. Selected BAC clones were grown in 200uL of 2xYT medium supplemented with suitable antibiotic (either cloramphenicol or kanamycin) in a 96 deep-well plate, for 24 hours at 37
2. with gentle shaking (320rpm). We added 40 uL of glicerol 87% (v/v) to the grown bacterial culture, shaked to ensure mixing and preserved at -80ºC.
3. We grew new plates from the glicerinated ones before extracting DNA from clones using a Millipore kit (Montage BAC96 Miniprep Kit, P36392, Rev. 08/01). BAC-end sequences
4. were obtained from the purified product.
5. The extracted DNA was amplified by DOP-PCR (R1 & R2, Fiegler et al., 2003, Genes, Chromosomes and Cancer, 36, 361-374).
6. Amplified products were purified using the Kit Montage PCR96 Plates, Millipore ref. MSNU03010.
7. Quantitation of the purified product was done with PicoGreen dsDNA Quantitation Kit (Molecular Probes, P-7589).
8. DNA was subjected to evaporation using a speed-vac, prior to adjust final concentration at 400ng/uL in spotting buffer (DMSO 50% v/v in water). DNA was then denatured at 99C
9. for 2 minutes. 8uL were placed on a spotting plate before depositing it on the surface of UltraGAPS Slides (Corning, 40015), using a VersArray Chip Writer spotter (BioRad).


title: Laccaria bicolor 4.9K ADNc macroarray

status: Public on Nov 23 2010

city: Champenoux

first: Francis

last: Martin

address: Route d'amance

department: EFPA

institute: INRA

organism: Laccaria bicolor

manufacture_protocol:
cDNA were amplified by PCR, purified on appropriate columns, and then prepared in 13 384-wells plates including some control spots (i.e. vectors used for cDNA cloning, external control cDNA, empty positions). Spotting was processed in denaturing conditions to array single stranded cDNA molecules. Arraying was processed by Eurogentec Array Service (Sarraing, BE) in 2005 with a BioGrid arrayer (384 pins) following manufacturer protocol
A total of 4992 features were spotted on 70 cm2 Nylon filters in 384 blocks (24 horizontal x 16 vertical, corresponding to the 384-wells plates). Within blocks of 4x4 mm, cDNA from plates 1 to 12 were respectively spotted at positions 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 of a 5x5 grid (5 horizontal x 5 vertical). These positions are given in the 'XDotsReader ID' column of platform file. The XDotsReader ID also provide block position: vertical position, A to P; horizontal position, 1 to 24.


title: Agilent-019921 Sheep Gene Expression Microarray (Feature Number version)

status: Public on Jul 22 2010

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Ovis aries

description:
Product Number: G4813A
Design ID: 019921
Arrays/Slide: 8 microarrays/slide
Format: 8 x 15K (One glass slide formatted with eight high-definition 15K arrays)
Sequences: 15,208 sheep probes represented

*** The ID column includes the Agilent Feature Numbers. A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL10778.

manufacture_protocol: Agilent 60-mer SurePrint technology.  See manufacturer's website www.agilent.com.


title: AB 5500 Genetic Analyzer (Caenorhabditis elegans)

last: GEO

organism: Caenorhabditis elegans


title: CGP Atlantic cod 20K oligo array v1.0

status: Public on Nov 05 2010

city: St. John's

first: Marije

last: Booman

state: NL

address: 1 Marine Lab Road

department: Ocean Sciences

institute: Memorial University of Newfoundland

organism: Gadus morhua

manufacturer: The Atlantic Microarray Facility at the Atlantic Cancer Research Institute (Moncton, NB, Canada)

first: Tudor

last: Borza

first: Charles

middle: Y

last: Feng

first: Tiago

middle: S

last: Hori

first: Brent

last: Higgins

first: Adrian

last: Culf

first: Daniel

last: Leger

first: Ian

last: Chute

first: Jennifer

middle: R

last: Hall

first: Anissa

last: Belkaid

first: Marlies

last: Rise

first: A

middle: K

last: Gamperl

first: Sophie

last: Hubert

last: Kimball

first: Rodney

last: Ouelette

first: Stewart

last: Johnson

first: Sharen

last: Bowman

first: Matthew

manufacture_protocol:
Array design: The array contains 20,000 oligos, each spotted in duplicate, representing unique contigs selected from the EST database which was established by the Atlantic Cod Genomics and Broodstock Development Project (CGP), accessible on request through www.codgene.ca. Also included are 1472 control features (cod actin, human actin, SpotReport Alien Oligos 4, 6, 7 an 8 (Stratagene) ands buffer-only spots), resulting in a total of 41,472 features on the array. All probes are in sense orientation.
Array Printing: Oligonucleotides were provided by IDT in Genetix X7022 384-well plates, each well containing 1 nmole of 50-mer oligo (dried). Oligos were resuspended in 30 μl of Schott Nexterion Spot printing buffer to a final oligo concentration of 30 μM. Oligos were spotted in duplicate on epoxy-coated glass slides (Schott Nexterion E slides) using a Genomic Solutions OmniGrid 100 microarray printer equipped with silicon print pins (Parallel Synthesis Technology SMT-S50). The array contains 41,472 features spotted on 48 blocks of 29 rows and 30 columns each (the last row of each block contains only 24 features).