title: Agilent-027020 100125_dmertens_180K_incl_linker 026678

status: Public on Jan 23 2017

city: Heidelberg

first: Katharina

last: Filarsky

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Arrays of this design have barcodes that begin with 16027020 or 2527020.

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 MiSeq (Caulerpa taxifolia)

status: Public on Apr 30 2015

last: GEO

country: USA

organism: Caulerpa taxifolia

technology: high-throughput sequencing

distribution: virtual


title: Illumina MiSeq (Brassica rapa)

organism: Brassica rapa


title: Illumina MiSeq (Ginkgo biloba)

organism: Ginkgo biloba


title: Illumina MiSeq (Nannochloropsis oculata)

organism: Nannochloropsis oculata


title: Ion Torrent PGM (Saccharomyces cerevisiae BY4741)

organism: Saccharomyces cerevisiae BY4741


title: CapitalBio Human LncRNA Microarray v2.0

status: Public on May 08 2015

city: Chengdu

first: Haixiang

last: Wu

address: No. 55, People’s South Road

department: Department of Ultrasonics

country: China

institute: the Second Hospital of Sichuan

technology: spotted DNA/cDNA


title: Illumina HiSeq 2500 (Ruminiclostridium thermocellum DSM 1313)

status: Public on Apr 29 2015

organism: Acetivibrio thermocellus DSM 1313


title: Illumina MiSeq (Triticum turgidum subsp. durum)

organism: Triticum turgidum subsp. durum


title: Qiagen Human miRNome miScript miRNA PCR arrays (V16.0, 384-well)

status: Public on Apr 28 2015

city: Ottawa

first: Kenny

last: Schlosser

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Nanostring Technologies -- custom design of a CodeSet of 299 probes

city: Geneva

first: Thomas

last: Matthes

address: Rue Gabrielle Perret-Gentil

department: Hematology

country: Switzerland

institute: Geneva University Hospital

technology: other

description: Nanostring assay; CodeSet produced by the manufacturer; sequences available at the manufacturer's Website


title: Illumina Genome Analyzer IIx (Camellia sinensis)

status: Public on Apr 24 2015

organism: Camellia sinensis


title: Illumina Genome Analyzer II (Rhizoctonia solani)

organism: Rhizoctonia solani


title: Agilent-027887 rek1

status: Public on Apr 27 2015

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

organism: Mus musculus

description:
Modification of previous hox tiling design to include extended hox regions.

Arrays of this design have barcodes that begin with 16027887 or 2527887.

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 MiSeq (Synthetic plasmid)

organism: Synthetic plasmid


title: Agilent-027887 rek1 (Probe Name Version)

distribution: commercial


title: Agendia32627_DPv1.14_SCFGplus

status: Public on Jan 04 2016

city: Amsterdam

first: Inès

last: Goossens-Beumer

address: Science Park 406

country: Netherlands

institute: Agendia NV

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


title: Agilent-031550 Homo sapiens 45K UroGenRa

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description:
Arrays of this design have barcodes that begin with 16031550 or 2531550.

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: TaqMan® OpenArray® Rodent MicroRNA Panel [4444909]

city: Boston

first: Andrew

middle: Michael

last: Siedlecki

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description: PCR assay

manufacture_protocol: see manufacturer's website. Mouse microRNA for qPCR analysis


title: Illumina HiSeq 2500 (Mycobacterium tuberculosis CDC1551)

organism: Mycobacterium tuberculosis CDC1551


title: Agilent Custom Lactobacillus Gene Expression  8x15k Array (AMADID: 067475) design

city: BARI

first: pasquale

last: filannino

address: Via Amendola, 165/A

department: Dipartimento di Scienze del Suolo

country: Italy

institute: Università degli Studi di Bari “Aldo Moro”

organism: Lactiplantibacillus plantarum

first: Pasquale

last: Filannino

first: Raffaella

last: Di Cagno

first: Maria

last: De Angelis

first: Marco

last: Gobbetti


title: MYcroarray_CAT_Neosartorya-fischeri-NRRL181_40K-3rep-V1

status: Public on Apr 23 2015

city: Ensenada

first: RAFAEL

last: VAZQUEZ DUHALT

state: Baja California

address: Km 107 Carretera Tijuana-Ensenada

department: Bionanotechnology

country: Mexico

institute: Nanoscience and Nanotechnology Center-UNAM

organism: Aspergillus fischeri NRRL 181

manufacture_protocol: in situ oligonucleotide synthesis using phosphoramidite chemistry and proprietary light directed synthesis. More information can be found here: http://www.mycroarray.com/technology/synthesis.html


title: URH-TALL_Bovine_Operon V1.1_2 [gene-level]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Bos taurus

technology: spotted oligonucleotide

distribution: non-commercial

first: Christine

last: Leroux

first: Séverine

last: Ollier

first: Lidwine

last: Trouilh

first: Laurence

last: Bernard

first: Muriel

last: Bonnet

first: Yves

last: Chilliard

manufacture_protocol: The Operon Bos taurus (bovine) AROS V1.1, which contains 8329 70-mer oligonucleotides representing 8329 genes from the Bos taurus genome (http://www.operon.com/arrays/oligosets_Bovine.php), completed with 53 genes chosen for their implication in mammary metabolism, and the Operon Bos taurus (bovine) AROS Controls (380 controls) were spotted in duplicate on UltraGAPS Coated Slides (Corning B.V. Life Sciences) at the Biochips platform of the Génopole Toulouse Midi-Pyrénées. Details can be found at http://biopuce.insa-toulouse.fr/protocoles.php#array_prep.


title: NanoString nCounter v1.7.0

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

manufacture_protocol: see manufacturer's website: http://www.nanostring.com/


title: Illumina HiSeq 2500 (Camponotus castaneus; Ophiocordyceps unilateralis)

status: Public on Apr 22 2015

last: GEO

organism:
Camponotus castaneus
Ophiocordyceps unilateralis


title: Illumina HiSeq 2500 (Ophiocordyceps unilateralis)

organism: Ophiocordyceps unilateralis


title: Agilent Brown planthopper (BPH) microarray version 2 (018781), containing partial spider mite EST

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

country: Japan

institute: National Institute of Agrobiological Sciences

organism:
Tetranychus urticae
Nilaparvata lugens


title: Illumina HiSeq 2500 (Camponotus castaneus)

organism: Camponotus castaneus


title: AB 5500xl Genetic Analyzer (Oryctolagus cuniculus)

organism: Oryctolagus cuniculus


title: Nucleic Acid Programmable Protein Array (NAPPA) BLBC discovery array-GST2

city: Tempe

first: Jie

last: Wang

state: Arizona

address: 1001 S. McAllister Ave.

department: Center for Personalized Diagnostics

institute: Arizona State University

organism: Homo sapiens

technology: spotted peptide or protein

description: The array was designed as 6 spots by 6 spots as a block, and 4 by 12 blocks across the whole arraythe order of spots on the array, thus one array includes 1728 spots. ID indicates the order of the spots.


title: Nucleic Acid Programmable Protein Array (NAPPA) BLBC discovery array-GST3


title: Nucleic Acid Programmable Protein Array (NAPPA) BLBC discovery array-FLAG


title: Illumina HiSeq 2000 (Anoplophora glabripennis)

organism: Anoplophora glabripennis


title: Agilent-022267 Streptococcus suis

status: Public on Apr 21 2015

city: shanghai

first: liping

last: feng

address: No. 3577 Jinke Rd., Shanghai

institute: Shanghai Laboratory Animal Research Center

organism: Streptococcus suis


title: Agilent-021634 Homo sapiens chr1-5 hg18

city: Atlanta

first: M. Katharine

last: Rudd

address: 1518 Clifton Rd, CNR 5043

department: Human Genetics

institute: Emory University School of Medicine

description:
chr1-5: 5Mb of p and q arms

Arrays of this design have barcodes that begin with 16021634 or 2521634.

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-040718 Homo sapiens May2012 hg19

description:
Arrays of this design have barcodes that begin with 16040718 or 2540718.

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 1500 (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: Agilent-037646 Homo sapiens translocations5BW hg19

description:
Arrays of this design have barcodes that begin with 16037646 or 2537646.

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 (Human herpesvirus 4)

organism: human gammaherpesvirus 4


title: Illumina HiSeq 2000 (Lactobacillus salivarius str. Ren)

status: Public on Apr 20 2015

organism: Ligilactobacillus salivarius str. Ren


title: Illumina HiSeq 2000 (Spodoptera litura)

organism: Spodoptera litura


title: Agilent-034386 Homo sapiens translocations1BW hg19

description:
Arrays of this design have barcodes that begin with 16034386 or 2534386.

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-034387 Homo sapiens translocations2BW 034386 hg19

description:
Arrays of this design have barcodes that begin with 16034387 or 2534387.

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-035730 Homo sapiens translocations4BW 035709 hg19

description:
Arrays of this design have barcodes that begin with 16035730 or 2535730.

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 (Tremella fuciformis)

status: Public on Apr 19 2015

organism: Tremella fuciformis


title: Illumina Genome Analyzer IIx (Waddlia chondrophila)

organism: Waddlia chondrophila


title: Nucleic Acid Programmable Protein Array (NAPPA) BLBC discovery array-GST4


title: Agilent-035709 Homo sapiens translocations3BW hg19

description:
Arrays of this design have barcodes that begin with 16035709 or 2535709.

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: Nucleic Acid Programmable Protein Array (NAPPA) BLBC discovery array-GST1


title: Illumina HiSeq 2000 (Saccharomyces cerevisiae S288c)

organism: Saccharomyces cerevisiae S288C


title: Illumina MiSeq (Streptococcus pyogenes MGAS15252)

status: Public on Apr 17 2015

organism: Streptococcus pyogenes MGAS15252


title: AB 5500xl Genetic Analyzer (Thalassiosira pseudonana)

status: Public on Apr 16 2015

organism: Thalassiosira pseudonana


title: RIBOBIO human 12K v1. 0

city: Changsha

first: Fengzhen

address: 87# Xiangya Road Changsha, Hunan 410008P.R.China

institute: Xiangya Hospital, Central South University

description: microRNA

manufacture_protocol: Oligonucleotide probes are designed by oligoarray. Probe length is 50 nt.


title: [MD4-9313a520062] Affymetrix Prochlorococcus marinus MED4 Array

status: Public on Apr 15 2015

city: Cambridge

first: Sallie

middle: W

last: Chisholm

address: 15 Vassar St., Bldg. 48-419

institute: MIT

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

manufacture_protocol: see manufacturer's web site


title: NimbleGen C. elegans 07114_CE2_WG_CGH_T

city: Albuquerque

first: Ulfar

last: Bergthorsson

state: New Mexico

address: 219 Yale Blvd NE

department: Biology

institute: University of New Mexico

organism: Caenorhabditis elegans

description: Genome build information: Wormbase WS120

manufacture_protocol: See manufacturer's website


title: SABiosciences Neurotrophin and Receptors RT²  profiler PCR array

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

institute: International Christian University

organism: Rattus norvegicus

description:
Neurotrophin and receptors
SABiosciences RT² Profiler PCR array


title: Reis-Filho Human 32K BAC

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

description: human genome assembly = GRCh37 for genomic coordinates

manufacturer: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK

manufacture_protocol: This platform comprises >32,000 BAC clones, spotted onto Corning GAPSII coated glass slides (Corning, NY, USA).


title: Illumina HiSeq 2000 (Lunularia cruciata)

organism: Lunularia cruciata


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S)


title: Illumina HiSeq 2000 (Marmota monax)

organism: Marmota monax


title: Illumina HiSeq 2500 (Sclerotinia sclerotiorum; Trichoderma hamatum GD12)

organism:
Sclerotinia sclerotiorum
Trichoderma hamatum GD12


title: Illumina HiSeq 2500 (Trichoderma hamatum GD12)

organism: Trichoderma hamatum GD12


title: Illumina Genome Analyzer II (Dirofilaria immitis)

status: Public on Apr 14 2015

organism: Dirofilaria immitis


title: Illumina HiSeq 2000 (Gigaspora rosea)

organism: Gigaspora rosea


title: Illumina HiSeq 2500 (Sclerotinia sclerotiorum)

organism: Sclerotinia sclerotiorum


title: Illumina HiSeq 2500 (Eucalyptus grandis)

organism: Eucalyptus grandis


title: [MoGene-2_1-st] Affymetrix Mouse Gene 2.1 ST Array [probe set (exon) version]

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Mus musculus

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

#%create_date=Wed Apr  2 20:07:33 2014 PDT
#%chip_type=MoGene-2_1-st-v1
#%lib_set_name=MoGene-2_1-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm10
#%genome-version-ucsc=mm10
#%genome-version-ncbi=38
#%genome-version-create_date=2011-12-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Mus musculus
#%genome-lifted_from-version-ucsc=mm10
#%genome-lifted_from-version-ncbi=38
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34

manufacture_protocol: See manufacturer's web site


title: 454 GS FLX (Eutrema salsugineum)

status: Public on Apr 10 2015

organism: Eutrema salsugineum


title: Illumina HiSeq 1500 (Escherichia coli)

organism: Escherichia coli


title: Illumina HiSeq 1000 (Lactobacillus buchneri CD034)

status: Public on Apr 13 2015

organism: Lentilactobacillus buchneri subsp. silagei CD034


title: Illumina MiSeq (Gigaspora rosea)


title: Agilent-031052 miRNA-v3.6-Multispecies-8x15K array

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

organism: synthetic construct


title: Gencode v15 lncrna.2 probe version1 Agilent Design ID (AMADID) 047718

status: Public on Apr 09 2015

city: Copenhagen

first: Aashiq

middle: H.

last: Mirza

state: Herlev

address: Herlev Ringvej 75

department: University of Copenhagen, Herlev Hospital

country: Denmark

institute: Center for non-coding RNA in Technology and Health

organism: Homo sapiens


title: 454 GS Junior (human gut metagenome)

organism: human gut metagenome


title: Illumina HiSeq 2000 (Rhizophagus irregularis DAOM 181602)

organism: Rhizophagus irregularis DAOM 181602=DAOM 197198


title: Agilent-022267 Streptococcus suis 05 8X15K Microarray (Probe Name version)

first: qian

last: jin

address: libing road

institute: MSP

organism: Streptococcus suis


title: 454 GS FLX (rat gut metagenome)

organism: rat gut metagenome


title: Illumina HiSeq 2000 (Populus deltoides)

organism: Populus deltoides


title: Illumina HiSeq 2000 (Populus balsamifera)

organism: Populus balsamifera


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [custom CDF: hugene10stv1_73_020.cdf]

status: Public on Apr 08 2015

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

description:
Probe set data extracted from custom CDF:
hugene10stv1_73_020.cdf

For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 74.


title: Illumina HiSeq 2000 (Botrytis cinerea; Vitis vinifera)

organism:
Vitis vinifera
Botrytis cinerea


title: Illumina HumanExome-12 v1.2 BeadChip

first: GEO

last: admin

technology: oligonucleotide beads

description:
HumanExome-12v1_2B

coverage of putative functional exonic variants selected from over 12,000 individual exome and whole-genome sequences

The exonic content consists of > 240,000 markers representing diverse populations—including European, African, Chinese, and Hispanic individuals—and a range of common conditions, such as type 2 diabetes, cancer, metabolic, and psychiatric disorders.

HumanExome BeadChips deliver focused coverage of exonic regions, but do not include coverage outside of coding regions. Researchers can use these arrays to obtain new insights from previously genotyped cohorts, or run new studies focused on identifying functionally relevant associations.


title: Ion Torrent Proton (Oreochromis niloticus)

organism: Oreochromis niloticus


title: Illumina HiSeq 2000 (Measles virus)

organism: Measles morbillivirus


title: Agilent Custom Arabidopsis 8x60k Microarray designed by Genotypic Technology Private Limited (AMADID: 48015)

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: Arabidopsis thaliana

manufacture_protocol: see www.chem.agilent.com


title: Illumina HiSeq 2000 (Neovison vison)

organism: Neogale vison


title: Illumina HiSeq 2500 (Solanum pimpinellifolium)

organism: Solanum pimpinellifolium


title: Illumina HiSeq 2500 (Solanum chilense)

organism: Solanum chilense


title: Illumina HiSeq 2000 (Zostera marina)

status: Public on Apr 03 2015

organism: Zostera marina


title: Illumina HiSeq 2000 (Helicobacter pylori 26695)

organism: Helicobacter pylori 26695


title: Illumina HiSeq 2500 (Helicobacter pylori 26695)


title: Illumina HiSeq 2000 (Drosophila sechellia)

status: Public on Apr 05 2015

organism: Drosophila sechellia


title: Homo sapiens Custom Human 8x15k Array designed by Genotypic Technology Private Limited (AMADID: 045815)

status: Public on Apr 02 2015

organism: Homo sapiens


title: Agilent-069979 Arraystar Mouse CircRNA microarray V1

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Mus musculus

description: Genome build: MM10


title: Illumina MiSeq (Streptococcus pyogenes)

last: GEO

organism: Streptococcus pyogenes


title: Illumina Genome Analyzer (Eucalyptus grandis)

organism: Eucalyptus grandis


title: Combimatrix 90k Custom bovine Microarray

status: Public on Apr 04 2015

city: Lodi

last: Trovato

address: Via Einstein

institute: Parco Tecnologico Padano

organism: Bos taurus

manufacturer: University of Verona - Biotechnology Department - Functional Genomics Centre

manufacture_protocol: 43,768 unique probes with a length of 35 nucleotides were designed, each representing a single bovine transcript. These probes were synthesized in duplicate, along with negative and quality controls.Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix. The Combimatrix standard protocol was used.


title: NimbleGen Rattus norvegicus Tiling Array [2006-08-10_RN34_WG_CGH]

status: Public on Apr 01 2015

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

organism: Rattus norvegicus

description:
Chromosomal genomic hybridization (CGH) custom design
Whole Genome Tiling of rat genome, n=385,102,   median 1395bps
whole genome tiling array of the rat genome with 385,102 probes per array. The probe size ranged from 50-75mer in length with median probe spacing of 1395bp.

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


title: Version 2 DGRC oligonucleotide microarrays

city: Kearney

first: Kimberly

middle: Ann

last: Carlson

state: NE

institute: University of Nebraska at Kearney

organism: Drosophila melanogaster

manufacturer: Drosophila Genomics Resource Center [DGRC], Bloomington, IN

manufacture_protocol:
1. Indirect labeling with Cy3/Cy5 fluorescent dyes was performed using 12 ug of total RNA per sample using the Superscript Indirect cDNA Labeling System for DNA Microarrays (Invitrogen).
2. All reagents and buffers used were included in the kit
3. Following reverse-transcription (RT), the resultant amino-allyl labeled cDNA was incubated with Cy3/Cy5 in DMSO to couple the Cy3 or Cy5 dyes to the cDNA to create fluorescently labeled probes
4. The CY3 and CY5 labeled probes were purified by gel-exclusion chromatography using SNAP columns (Invitrogen).
5. Prior to hybridization, the microarray slides were pre-hybridized for 45 minutes at 42°C in 3X SSC solution (3 M NaCl, 0.3 M sodium citrate, 1 mM EDTA) containing 1% bovine serum albumin
6. The Cy3 and Cy5 probes were mixed together in 40 ul Ambion hybridization buffer #2 (Ambion)
7. Blocking agents that included poly-dA (20 ug) and Cot-1 DNA (20 ug) were added
8. Hybridization was performed overnight at 42°C
9. After hybridization, the slides were washed 2x times with 2.0x SSC, 0.5% SDS at 42 degrees for 15 minutes
10.  slides were washed then 2x with 0.5x SSC, 0.50% SDS for 15 minutes each


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [CDF: Brainarray Version 15.1.0, MoEx10stv1_Mm_ENSG]

city: Helsinki

first: Maria

last: Jussila

state: Helsinki

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

manufacture_protocol: This is identical to GPL14363 but done using ENSG CustomCDF Version 15.1.0 gene descriptions for normalization. Gene ID:s are based on EnsEMBL Mus musculus release 65.


title: Arraystar Mouse CircRNA microarray

description: Genome build: MM10

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


title: Agilent-041183 TurbotV2_SSFN microarray2013 [Probe Name Version]

city: Vigo

first: Patricia

last: Pereiro

state: Pontevedra

address: C/Eduardo Cabello, 6

department: Immunology and Genomics

country: Spain

institute: IIM-CSIC

organism: Scophthalmus maximus

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


title: Agilent-048608 Hypomesus transpacificus DSmelt V01_April 1st 2013_Connon 048604

city: Davis

first: Lisa

last: Komoroske

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

organism: Hypomesus transpacificus

description:
Agilent 4x44K oligo array
Delta smelt (hypomesus transpacificus) Version.01

Arrays of this design have barcodes that begin with 16048608 or 2548608.

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-036891 Babesia bovis_UP array

city: Pretoria

first: Ingrid

last: Rossouw

state: Gauteng

address: Lynnwoodroad

department: Genetics

country: South Africa

institute: University of Pretoria

organism: Babesia bovis

manufacture_protocol:
Custom B. bovis microarray slides were manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers were deposited uniformly onto specially-prepared glass slides. This in situ synthesis process printed 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enabled the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry was used in the reactions which allowed for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. The general cycle and process of oligo synthesis was repeated 60 times.
Features were 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: [HG-U219] Affymetrix Human Genome U219 Array [CDF: Brainarray HGU219_Hs_ENTREZG_17.0.0]

status: Public on Aug 20 2014

city: Bethesda

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This identical to GPL13667 but a custom cdf environment was used to extract data.

manufacture_protocol: see manufacturer's website


title: Agilent-037331 Copy_of_C. albicans assembly 21_017942 (Feature ID)

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

institute: University of Lausanne and University Hospital Center

organism: Candida albicans

manufacture_protocol: Oligonucleotides were designed the 27th of October 2007 according with the latest Candida albicans annotation from CGD (http://www.candidagenome.org) assembly 21, using eArray from Agilent Technology (Design ID 037331). Each of 6101 open reading frames is represented by two oligonucleotides probes. Mitochondrial genes are indicated by the prefix CaalfMp. The probes were used to generate custom microarrays in a 4x44 K format with a randomized layout.


title: Illumina HiSeq 2000 (Citrus reticulata)

organism: Citrus reticulata


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium)

status: Public on Apr 25 2013


title: Arraystar Human CircRNA microarray

description: Genome build: HG19


title: NimbleGen Rattus norvegicus Tiling Array [120821_RN34_Economy_01/02_UX1 array]

description:
Whole Genome Tiling of rat genome with 2 different array sets, n=4,085,426 per sub-array,   median 300 bp
whole genome tiling array of the rat genome array which contains 2 different array set, with 4,085,426 probes per sub-array.  Probe sizes range from 50-75 bp in length with the median probe spacing of 300 bp.


title: Illumina HiSeq 1500 (Danio rerio)

status: Public on Jan 15 2014

organism: Danio rerio


title: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [HuGene21st_Hs_ENTREZG_19.0.0]

description:
Brainarray: HuGene21st_Hs_ENTREZG_19.0.0
Brainarray_website: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp


title: Illumina HiSeq 2000 (Chlamydomonas reinhardtii)

status: Public on Aug 10 2012

organism: Chlamydomonas reinhardtii


title: URH-TALL_Bovine_Operon V1.1_2

status: Public on Jul 02 2007

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

country: France

institute: INRA

first: Séverine

last: Ollier

first: Lidwine

last: Trouilh

first: Laurence

last: Bernard

first: Muriel

last: Bonnet

first: Yves

last: Chilliard

manufacture_protocol: The Operon Bos taurus (bovine) AROS V1.1, which contains 8329 70-mer oligonucleotides representing 8329 genes from the Bos taurus genome (http://www.operon.com/arrays/oligosets_Bovine.php), completed with 53 genes chosen for their implication in mammary metabolism, and the Operon Bos taurus (bovine) AROS Controls (380 controls) were spotted in duplicate on UltraGAPS Coated Slides (Corning B.V. Life Sciences) at the Biochips platform of the Génopole Toulouse Midi-Pyrénées. Details can be found at http://biopuce.insa-toulouse.fr/protocoles.php#array_prep.


title: Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version)

status: Public on Feb 02 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Arabidopsis thaliana

description:
Arabidopsis 4 Oligo Microarray (V4)

Arrays of this design have barcodes that begin with 16021169 or 2521169.

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 Probe Names.

A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL9020.


title: Illumina Genome Analyzer II (Saccharomyces cerevisiae)

status: Public on Oct 07 2009

organism: Saccharomyces cerevisiae