title: Agilent-048674 Nannochloropsis oceanica CCMP1779

status: Public on May 31 2017

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

organism: Nannochloropsis oceanica

technology: in situ oligonucleotide

description:
Nannochloropsis oceanica CCMP1779

Arrays of this design have barcodes that begin with 16048674 or 2548674.

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 (Parascaris univalens)

last: GEO

country: USA

organism: Parascaris univalens

technology: high-throughput sequencing

distribution: virtual


title: Exiqon miRCURY LNATM microRNA Array, v.11.0

status: Public on May 30 2017

city: Miami

first: Eliana

middle: C

last: Martinez

state: FL

address: 1501 N.W. 10th Avenue. BRB 803

institute: University of Miami Miller School of Medicine

organism: Rattus norvegicus

technology: spotted oligonucleotide

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


title: Custom Agilent-021088 C. elegans expression microarray

status: Public on Dec 04 2017

city: Barcelona

first: Ben

last: Lehner

address: Carrer Doctor Aiguader, 88

department: systems biology

country: Spain

institute: CRG

organism: Caenorhabditis elegans

manufacture_protocol: Standard Agilent Protocol


title: Illumina HiSeq 2500 (Homo sapiens; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Homo sapiens


title: Illumina HiSeq 2500 (Drosophila melanogaster; Mus musculus; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Mus musculus


title: Illumina HiSeq 2500 (Drosophila melanogaster; Homo sapiens; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens


title: Illumina HiSeq 2500 (Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens)

organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens


title: Agilent-021441 NCode Human Long Non-coding RNA microarray (Custom Annotation)

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

organism: Homo sapiens

description: Custom annotation was obtained by direct matching of the probeseqs of the Agilent-021441 NCode Human Long Non-coding RNA microarray to the human transcriptome (Gencode.V23). These annotations are more accurate than the original annotation issued by the manufacturer.

manufacture_protocol: This array targets 17,112 putative long noncoding RNAs and 22,074 coding RNA transcripts. 60-mer probes were designed using Agilent's probe design system and printed using Agilent SurePrint technology. Spots re 65μM in site.


title: NanoString nCounter Human miRNA Expression Assay, V3A

status: Public on Nov 21 2018

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

technology: other

manufacture_protocol: See manufacture's website http://www.nanostring.com/


title: Arraystar Human LncRNA microarray V2.0 (Agilent-033010; custom-annotation)

description:
This annotation was obtained by direct matching of the probeseqs of the Arraystar Human LncRNA microarray V2.0 (Agilent-033010) [GPL13825] to the human transcriptome (Gencode.V23) and is more accurate than the original annotation issued by the manufacturer.

ArrayStar Human LncRNA Microarray V2.0 is designed for the global profiling of human LncRNAs and protein-coding transcripts. 33,045 LncRNAs and 30,215 coding transcripts can be detected by our second-generation LncRNA microarray. The LncRNAs are carefully collected from the most authoritative databases such as RefSeq, UCSC knowngenes, Ensembl and many related literatures. Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

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


title: Illumina HiSeq 4000 (Locusta migratoria)

status: Public on May 25 2017

organism: Locusta migratoria


title: NanoString nCounter Cancer CN Panel Assay

status: Public on May 27 2017

city: Toronto

first: Dorota

last: Sendorek

state: ON

address: 661 University Ave, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

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


title: RiboArray™genDETECT™ Human Array 1X40K

city: Beijing

first: Shi

last: Juan

address: 5 Dong Dan San Tiao

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College


title: Complete Genomics (Homo sapiens)

status: Public on May 29 2017


title: Single cell QRT-PCR analysis of PND7 mice endometrial epithelial cells

status: Public on Jun 29 2017

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

organism: Mus musculus

technology: RT-PCR

description:
PCR assay
sinlge cell Q-RT-PCR

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2500 (Paralichthys olivaceus)

status: Public on May 26 2017

organism: Paralichthys olivaceus


title: Illumina HiSeq 2500 (Arabis alpina)

organism: Arabis alpina


title: Agilent-035550 UniversityPadova_Ruditapes decussatus_8x15K_v4

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

organism: Ruditapes decussatus

description: A total of 41,119 contigs of R.decussatus obtained in the previous study (see Leite et al. 2013 for details) were reannotated to design a new version of R. decussatus DNA microarray. The Basic Local Alignment Search Tool (BLAST) was used to perform annotation of R. decussatus contigs. Batch Blast similarity searches for the entire set of contigs were locally conducted against NCBI (National Centre for Biotechnology Information) amino acidic non redundant (nr) database using Blastx option. To improve the number of annotated contigs five different approaches were attempted: i) blastx searches (cut off e-value of < 1.0 E-3) against protein database UniProtKB/SwissProt, ii) blastx (cut off e-value of < 1.0 E-3) and blastn (cut off e-value of < 1.0 E-5) searches against proteins and high quality draft trascriptomes of Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, Tetraodon nigroviridis, Homo sapiens, Bos taurus, Mus musculus, Xenopus tropicalis, Drosophila melanogaster, Aedes aegypti, Aedes mellifera, Schistosoma mansoni, Caenorhabditis elegans, Ciona intestinalis, Ciona savignyi, Culex quinquefasciatus available on Ensembl Genome Browser, iii) blastx (cut off e-value of < 1.0E-3) and blastn (cut off e-value of < 1.0 E-5) searches against proteins, transcripts and assembly scaffolds of Lottia gigantea v1.0 database and Crassostrea gigas. The Gene Ontology (GO) terms associations for BP, MF and CC were performed using Blastx algorithm against the NCBI amino acid nr database implemented in Blast2GO software.   Probe design started with the selection of target sequences to be represented onto the R. decussatus   microarray. All annotated entries (13,161 corresponding to the 32% of total contigs) were included. As most sequence reads were obtained from a non directional cDNA library, sense strand orientation was inferred putatively from that of homologuous protein sequences of other species. Accordingly, one probe for annotated transcripts with known orientation was designed to construct a high-density oligo-DNA microarray, while two probes with both orientations were designed for contigs with ambiguous orientation. Probe design was carried out using the Agilent eArray interface, which applies proprietary prediction algorithms to design 60 mer oligoprobes. Microarrays were synthesized in situ using the Agilent ink-jet technology with a 8 × 15 K format. Each array included default positive and negative controls.  A total of 14,003 probes, representing 13,161 R. decussatus transcripts were successfully obtained.  Independent probes are named withunivocal ID; the anti-sense probes are distinguished by suffix _AS. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology.

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


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [CDF: hugene10st_Hs_ENTREZG_20]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: hugene10st_Hs_ENTREZG_20

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

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Hibiscus syriacus)

organism: Hibiscus syriacus


title: Human nuclear tRNA array

status: Public on May 24 2017

city: Glasgow

first: Sebastian

last: Kirchner

address: 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

manufacturer: Frauenhofer Institute for Biomedical Research (Potsdam, Germany); Intergrated Genomics Inc. (Chicago, USA)

manufacture_protocol:
1. Oligos were arrayed in 384 well plates with a final concentration of 10 µM in 3× SSC/0.01% SDS in a total volume of 25 µl.
2. Arrays were printed onto (3-Glycidyloxypropyl)trimethoxysilane (Sigma) activated glas slides using a contact-spotter (QArray 2, Moleculare Devices).
3. After spotting arrays were incubated overnight at 4°C in a humidified atmosphere and subsequently dried for 30 min at 30°C.
4. Arrays were stored in a dry atmosphere at room temperature until use.


title: Illumina HiSeq 4000 (Heterodera avenae)

status: Public on May 23 2017

organism: Heterodera avenae


title: [MoGene-2_1-st] Affymetrix Mouse Gene 2.1 ST Array [CDF: mogene21st_Mm_ENTREZG_18.0.0]

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

institute: King's College London

description: This array is identical to GPL17400 but the data were analyzed with a custom CDF environment.

relation: Alternative to: GPL17400 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: AB 5500xl Genetic Analyzer (phototrophic enrichment cultured UCC-O)

organism: phototrophic enrichment culture UCC-O


title: Illumina MiSeq (Mycobacterium phage L5)

status: Public on May 22 2017

organism: Fromanvirus L5


title: NextSeq 550 (Mus spretus)

organism: Mus spretus


title: Illumina MiSeq (Mycobacterium phage StarStuff)

organism: Mycobacterium phage StarStuff


title: Illumina MiSeq (Mycobacterium phage D29)

organism: Fromanvirus D29


title: Illumina HiSeq 2000 (Anser anser)

organism: Anser anser


title: Illumina HiSeq 2500 (Sulfolobus islandicus REY15A)

status: Public on May 19 2017

organism: Saccharolobus islandicus REY15A


title: Plants miRNA Array miRPlants_19_NJAU_121101a [index version]

status: Public on May 20 2017

city: Suzhou

first: Jiajia

last: Chen

address: Kerui Road

institute: Suzhou University of Science and Technology

organism: Embryophyta

description: The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.


title: HiSeq X Ten (Sulfolobus islandicus REY15A)


title: Brassica napus (Oilseed Rape) miRNA Array (v. miROilseedRape_ZJU_130917)

status: Public on May 16 2017

city: Hangzhou

first: cao

last: jiayi

address: 866 Yu Hang Tang Road

organism: Brassica napus

distribution: commercial

manufacture_protocol: Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.;Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.


title: BGISEQ-500 (Citrus sinensis)

status: Public on May 17 2017

organism: Citrus sinensis


title: BGISEQ-500 (Citrus trifoliata)

organism: Citrus trifoliata


title: BGISEQ-500 (Citrus junos)

organism: Citrus junos


title: Ion Torrent Proton (Candida parapsilosis)

organism: Candida parapsilosis


title: Illumina HiSeq 2500 (Lactobacillus plantarum)

organism: Lactiplantibacillus plantarum


title: Illumina NextSeq 500 (Glossina palpalis)

organism: Glossina palpalis


title: Illumina HiSeq 2000 (Rhodotorula mucilaginosa)

status: Public on May 15 2017

organism: Rhodotorula mucilaginosa


title: BGISEQ-500 (Boehmeria nivea)

organism: Boehmeria nivea


title: Illumina HiScanSQ (Nicotiana tabacum)

organism: Nicotiana tabacum


title: Illumina HiSeq 3000 (Glycine max)

organism: Glycine max


title: Illumina HiSeq 1000 (Malus domestica)

status: Public on May 12 2017

organism: Malus domestica


title: SABiosciences Human Tumor Metastasis PCR Array

city: Detroit

first: Karen

last: Beningo

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

organism: Homo sapiens

description: PCR assay


title: SABiosciences Human Cell Motility PCR Array

description: PCR assay


title: Illumina HiSeq 2000 (Triticum urartu x Aegilops tauschii)

status: Public on May 11 2017

organism: Triticum urartu x Aegilops tauschii


title: Illumina MiSeq (Bacillus subtilis subsp. subtilis str. 168)


title: Illumina NextSeq 500 (Nicotiana tabacum)


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version, custom CDF]

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

institute: GenomeDx

manufacture_protocol: See manufacturer's web site.


title: Illumina MiSeq (Geobacillus stearothermophilus)

organism: Geobacillus stearothermophilus


title: Agilent-045129 Boleae_FINAL

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

organism: Bactrocera oleae

description:
Bactrocera oleae transciptome microarray

Arrays of this design have barcodes that begin with 16045129 or 2545129.

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 (Aegilops longissima x Triticum urartu)

last: GEO

organism: Aegilops longissima x Triticum urartu


title: Agilent-025503 PerouLab_Mouse_4X180K_Custom_V1 [Probe Name version]

status: Public on May 10 2017

city: Chapel ill

first: Stephen

middle: D

last: Hursting

state: NC

address: 135 Dauer Drive

institute: University of North Carolina at Chapel Hill

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16025503 or 2525503.

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 Name.

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 (Exiguobacterium sibiricum)

organism: Exiguobacterium artemiae


title: Illumina HiSeq 2500 (Papio anubis)

organism: Papio anubis


title: Illumina HiSeq 4000 (Litchi chinensis)

status: Public on May 09 2017

organism: Litchi chinensis


title: Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version, hg19/GRCh37)

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

description: Platform data table annotations based on genome build hg19/GRCh37.

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


title: Illumina MiSeq (Planococcus halocryophilus)

organism: Planococcus halocryophilus


title: Illumina HiSeq 4000 (Triticum aestivum)

organism: Triticum aestivum


title: Illumina HiSeq 2500 (Delphinapterus leucas)

organism: Delphinapterus leucas


title: Illumina NextSeq 500 (Caenorhabditis elegans; Homo sapiens)

organism:
Caenorhabditis elegans
Homo sapiens


title: Illumina MiSeq (Paenibacillus riograndensis)

organism: Paenibacillus riograndensis


title: Illumina HiSeq 2500 (Micractinium conductrix)

organism: Micractinium conductrix


title: Illumina HiSeq 2500 (Chlorella sorokiniana)

organism: Chlorella sorokiniana


title: Illumina HiSeq 4000 (Toxoplasma gondii)

organism: Toxoplasma gondii


title: Illumina HiSeq 2000 (Citrus hindsii)

organism: Citrus hindsii


title: Illumina HiSeq 2000 (Aegilops longissima)

organism: Aegilops longissima


title: Illumina NextSeq 500 (Vanessa cardui)

status: Public on May 08 2017

organism: Vanessa cardui


title: Illumina MiSeq (Oryzias latipes)

organism: Oryzias latipes


title: Illumina HiSeq 2000 (Triticum urartu)

organism: Triticum urartu


title: Illumina HiSeq 3000 (Drosophila melanogaster; Mus musculus)

organism:
Drosophila melanogaster
Mus musculus


title: Illumina HiSeq 2000 (Lupinus digitatus)

organism: Lupinus digitatus


title: Illumina HiSeq 2000 (Lupinus pilosus)

organism: Lupinus pilosus


title: Illumina HiSeq 2000 (Lupinus cosentinii)

organism: Lupinus cosentinii


title: Illumina HiSeq 2000 (Lupinus angustifolius)

organism: Lupinus angustifolius


title: Illumina NextSeq 500 (Junonia coenia)

organism: Junonia coenia


title: Illumina HiSeq 2000 (Lupinus micranthus)

organism: Lupinus micranthus


title: Illumina HiSeq 2500 (Vernicia fordii)

organism: Vernicia fordii


title: Illumina HiSeq 2000 (Lupinus luteus)

organism: Lupinus luteus


title: Illumina HiSeq 3000 (Sulfolobus acidocaldarius)

status: Public on May 03 2017

organism: Sulfolobus acidocaldarius


title: LC Sciences Eggplant miRNA Array

status: Public on May 06 2017

city: Nanning

first: Wang

last: Yikui

address: north road

institute: Institute Of Vegetable Research, Guangxi Academy Of Agricultural Sciences

organism: Macrobrachium nipponense

description: Version No. miREggplant_GAAS


title: Illumina HiSeq 2000 (Lupinus albus)

organism: Lupinus albus


title: Geochip 4.2

status: Public on May 04 2017

city: Xiamen

first: Yu

last: Wang

address: Xiangan Nan Road

institute: Xiamen University

organism: Bacteria


title: Illumina HiSeq 2500 (Phymatosorus cuspidatus)

status: Public on May 01 2017

organism: Microsorum cuspidatum


title: Illumina HiSeq 2500 (Cyrtomium fortunei)

organism: Cyrtomium fortunei


title: Agilent-017642 and Agilent-020582 4x44K Format Aspergillus terreus

city: Åbo

first: Elina

last: Palonen

address: Artillerigatan 6

department: Biochemistry, Faculty of Science and Engineering

country: Finland

institute: Åbo Akademi University

organism: Aspergillus terreus NIH2624

description:
This platform represents the custom Agilent array for the original design (017642) and the updated design (020582).  Both designs contain identical probe sequences   (with identical probe IDs) except for two additional probes that were added to the first, original design (017642), resulting in the updated version (020582).

While the probe names and probe sequences are identical between the two versions, the feature number associated with each probe name on each version is different.

The accession string information in the raw data files for these arrays was derived from Neurospora crassa gene database and was included since A. terreus had no EST data available. However, the probe sequences were derived from the sequenced A. terreus strain NIH2624. Please see the 'Aspergillus terreus GeneName' column for the A. terreus gene IDs associated with the probe name and probe sequences.

manufacture_protocol: The microarray probes were designed using Agilent eArray application. Two 60-mer sense and 3' biased probes per gene were constructed in duplicate on the slide (4 technical replicates). See manufacturer's web site at http://www.agilent.com/ for further information.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 18.0.0]

status: Public on May 05 2017

organism: Homo sapiens

description: CDF downloaded from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/ensg.asp

relation: Alternative to: GPL570 (official version)


title: Illumina HiSeq 2000 (Lactococcus lactis)

organism: Lactococcus lactis


title: Illumina HiSeq 2500 (Streptococcus mutans UA159)

organism: Streptococcus mutans UA159


title: Agilent-015747 Zebrafish 44K Oligo Microarray (Probe name version)

city: Raleigh

first: Dereje

middle: D.

last: Jima

address: 850 Campus Drive

department: Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC)

institute: North Carolina State University

organism: Danio rerio

description:
Grid_GenomicBuild = danRer2:SangerZv4:June2004
FeatureExtractor_DesignFileName = 015747_D_F_20070117.xml


title: Illumina HiSeq 2500 (Pteris vittata)

organism: Pteris vittata


title: Illumina HiSeq 2500 (Diplazium esculentum)

organism: Diplazium esculentum


title: Illumina HiSeq 4000 (Anolis carolinensis)

organism: Anolis carolinensis


title: Illumina HiSeq 2500 (Microlepia platyphylla)

organism: Microlepia platyphylla


title: Illumina HiSeq 2500 (Odontosoria chinensis)

organism: Odontosoria chinensis


title: Illumina HiSeq 2500 (Alsophila spinulosa)

organism: Alsophila spinulosa


title: [Agilent-048448] Agilent 15Kx8 Thalassiosira pseudonana CCMP1335 array

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

institute: Norwegian University of Science and Technology

organism: Thalassiosira pseudonana CCMP1335

description: Agilent design ID: Agilent-048448

distribution: non-commercial

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


title: Agilent-036901 CytoSure Haematological Cancer and SNP Array 8x60k (Probe name version)

status: Public on May 02 2017

city: Warsaw

first: Beata

last: Grygalewicz

address: 15B Wawelska str

country: Poland

institute: Cancer Center and Institute of Oncology

description:
Genome build: hg19
CytoSure Haematological Cancer and SNP Array (8x60k) (Oxford Gene Technology (OGT, Yarnton, Oxford OX5 1PF UK))

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


title: Illumina HiSeq 2500 (Salvinia cucullata)

organism: Salvinia cucullata


title: Illumina HiSeq 2500 (Salvinia molesta)

organism: Salvinia molesta


title: Illumina HiSeq 2500 (Dicranopteris pedata)

organism: Dicranopteris pedata


title: Illumina HiSeq 2500 (Azolla caroliniana)

organism: Azolla caroliniana


title: Illumina HiSeq 2500 (Vandenboschia striata)

organism: Trichomanes striatum


title: Illumina HiSeq 4000 (Pan troglodytes)

organism: Pan troglodytes


title: Illumina HiSeq 2500 (Angiopteris fokiensis)

organism: Angiopteris fokiensis


title: Illumina HiSeq 2500 (Lygodium japonicum)

organism: Lygodium japonicum


title: Illumina HiSeq 2500 (Asplenium nidus)

organism: Asplenium nidus


title: Illumina HiSeq 2500 (Cibotium barometz)

organism: Cibotium barometz


title: Illumina HiSeq 2500 (Psilotum nudum)

organism: Psilotum nudum


title: Illumina HiSeq 2500 (Equisetum ramosissimum)

organism: Equisetum ramosissimum


title: Illumina HiSeq 2500 (Isoetes sinensis)

organism: Isoetes sinensis


title: Illumina HiSeq 2500 (Selaginella uncinata)

organism: Selaginella uncinata


title: Illumina HiSeq 1000 (Zea mays)

organism: Zea mays


title: Illumina HiSeq 2500 (Spodoptera frugiperda ascovirus 1a)

organism: Spodoptera frugiperda ascovirus 1a


title: Illumina HiSeq 2500 (Diplopterygium chinense)

organism: Diplopterygium chinense


title: Agilent-064456 C violaceum microarray 064455

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

country: Brazil

institute: Universidade de Sao Paulo

organism: Chromobacterium violaceum ATCC 12472

description:
Arrays of this design have barcodes that begin with 16064456 or 2564456.

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 2500 (Plenasium vachellii)

organism: Plenasium vachellii


title: Illumina HiSeq 2500 (Ophioglossum vulgatum)

organism: Ophioglossum vulgatum


title: Illumina HiSeq 2500 (Palhinhaea cernua)

organism: Palhinhaea cernua


title: Illumina HiSeq 2500 (Selaginella moellendorffii)

organism: Selaginella moellendorffii


title: CapitalBio 36K Mouse Genome Array

status: Public on Feb 08 2011

first: Yiqiang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

organism: Mus musculus

description:
Oligos (Operon) are designed from Mouse Ensembl release 26.33b.1, NCBI RefSeq, RIKEN full-length clone sequences, and other GenBank sequences.
Ensembl: http://www.ensembl.org
NCBI: http://www.ncbi.nlm.nih.gov
RIKEN: http://fantom.gsc.riken.jp
The pathway and GO annotation were added by CapitalBio Corporation with the information from KEGG and GOA.

manufacture_protocol: As described in the CapitalBio Corporation Manual.


title: Illumina HiSeq 4000 (Gallus gallus)

status: Public on May 22 2017

organism: Gallus gallus


title: Exiqon miRCURY LNA microRNA array, 7th generation REV [miRBase v18.0, condensed Probe_ID version]

status: Public on Dec 27 2013

city: Bengbu

first: yiwen

last: zhang

state: Anhui

address: 287 Chang Huai Road

department: Hematology

institute: The First Affiliated Hospital of Bengbu Medical College

organism: Homo sapiens


title: Illumina HiSeq 2500 (Streptococcus agalactiae)

organism: Streptococcus agalactiae


title: Illumina HiSeq 2000 (Arabis alpina)

status: Public on Nov 08 2016

organism: Arabis alpina


title: Illumina HiSeq 2500 ([Candida] glabrata; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus


title: Agilent-072445 ArrayXS_S.gallolyticus_01-2015 [gene version]

status: Public on Mar 22 2017

city: Bad Oeynhausen

first: Imke

last: Grimm

address: Georgstraße 11

department: Institut für Laboratoriums- und Transfusionsmedizin

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

organism: Streptococcus gallolyticus subsp. gallolyticus

description:
exp. val. 8x15K design for the S. gallolyticus strains UCN34, DSM 16831, ATCC BAA2069 and ATCC 43143, annotation preferentially based on ATCC BAA-2069
Arrays of this design have barcodes that begin with 16072445 or 2572445.
Probe sequences are available in the file GPL23196_072445_D_GEO_20150113.txt.gz located at the foot of this page.


title: Affymetrix human custom array [CDF: ADXCRCG2a520319]

city: Belfast

first: Philip

last: Dunne

address: Lisburn Road

institute: Queens University Belfast

description:
Almac Diagnostics Colorectal Cancer DSATM research tool
ADXCRCG2a520319

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


title: JPT PepStar™ Peptide Microarrays_Neisserial Heparin Binding Antigen (NHBA) variants

status: Public on May 27 2016

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

institute: GSK Vaccines

organism: Neisseria meningitidis serogroup B

technology: spotted peptide or protein


title: [At35b_MF] Affymetrix Arabidopsis Tiling 1.0F Array

status: Public on Sep 24 2010

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Arabidopsis thaliana

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


title: [At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array


title: Agilent-016322 Yeast (V2) Gene Expression 8x15K Microarray (Probe Name version)

status: Public on Nov 05 2012

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Saccharomyces cerevisiae

description:
Probe Name version of GPL9825

15,208 S. cerevisiae (S288C strain) ORFs represented.
Contents sourced from Saccharomyces Genome Database (SGD), January, 2004.

This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, and response to drug candidates.

*** A different version of this platform with the Agilent Feature Numbers in the ID column is assigned accession number GPL9825.

manufacture_protocol:
Agilent 60-mer SurePrint technology.
See manufacturer's web site at http://www.agilent.com/.


title: [miRNA-1] Affymetrix Multispecies miRNA-1 Array

status: Public on Jul 01 2009

organism: synthetic construct

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=Tue Oct 21 17:29:14 PDT 2008
#%guid=0000050091-1224635354-0064538561-0684514888-1962062125
#%chip_type=miRNA-1_0
# File contains all miRNAs from miRBase that have mapping information grouped by organism, all miRNAs without mapping information grouped by organism (designated as Sequence Type: miRNA), all sno/sca from UCSC (snoRNABase) and Ensembl (designated as Sequence Type: CDBox, HAcaBox, snoRNA and scaRna, and controls).
# miRNAs:
# * An annot name generally represents one genome location, but may refer to multiple annotations because of multiple mature products delineated by "-3p" and "-5p", or ".1" and ".2".
# * Also, those with a '-star' are minor products, and those without '-star' or any other aforementioned suffix are considered the major product.
# * Probeset IDs may appear more than once because the miRNA was mapped to multiple locations in the genome, and the annot names may have a "-1", "-2", etc type of suffix.
# * Probeset IDs with a letter suffix (eg, fru-miR-23a and fru-miR-23b) are related miRNAs where the sequence is highly similar.
# sno/sca:
# * The sequences for the sno/sca probesets are the entire sequences sent to Chip Design, not just the SIF regions.


title: [miRNA-2] Affymetrix Multispecies miRNA-2 Array

status: Public on Oct 07 2011

description:
#%create_date=Wed Dec 22 13:03:44 PST 2010
#%guid=04795ed5-9038-4dff-957e-da346791f552
#%chip_type=miRNA-2_0
# File order is all miRNAs that have mapping information grouped by organism, then all miRNAs without mapping information grouped by organism, then all sno/sca from UCSC and ensembl, and lastly the controls.
# miRNAs:
#  An annot name generally represents one genome location," but may refer to multiple annotations because of multiple mature products delineated by ""-3p"" and ""-5p"""," or "".1"" and "".2""."
#  Also, those with a '*' are minor products, and those without '*' or any other aforementioned suffix are considered the major product.
#  Probeset IDs may appear more than once because the miRNA was mapped to multiple locations in the genome," and the annot names may have a ""-1"""," ""-2""", etc type of suffix.
#  Probeset IDs with a letter suffix (eg, fru-miR-23a and fru-miR-23b) are related miRNAs where the sequence is highly similar.
#  pre-miRNA transcript probesets are designated with the prefix ""hp_"""
#  The annotations ""Human"," mouse and rat""",18-Oct-10,"Affymetrix normalization control mRNAs. 100 each for human, mouse and rat", are the verbatim probes and probeset id's as they appear on the respective 3-primeIVT mRNA expression arrays (U133, U230 and U430),,,,
# sno/sca:
#  The sequences for the sno/sca and hairpin probesets are the entire sequences sent to Chip Design, not just the SIF regions.


title: [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array

status: Public on May 13 2006

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

The GeneChip® Human Mapping 500K Array Set provides consistently high coverage across different populations. It is comprised of two arrays, each capable of genotyping on average 250,000 SNPs (approximately 262,000 for Nsp arrays and 238,000 for Sty arrays).


title: [miRNA-4] Affymetrix Multispecies miRNA-4 Array

status: Public on Aug 25 2014

description:
#%chip_type=miRNA-4_0 or miRNA-4_1
#%create_date=Tue May 13 14:16:15 PDT 2014
#%miRBase_version=v20

relation: Alternative to: GPL21572 (ProbeSet ID version)


title: [miRNA-4] Affymetrix Multispecies miRNA-4 Array [ProbeSet ID version]

status: Public on Mar 09 2016

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

relation: Alternative to: GPL19117 (ProbeSet Name version)