title: Illumina HiSeq 2000 (Cercospora zeina)

status: Public on Nov 30 2016

last: GEO

country: USA

organism: Cercospora zeina

technology: high-throughput sequencing

distribution: virtual


title: Drosophila 147 microRNA version 13

status: Public on Dec 18 2017

city: Tucson

first: Daniela

middle: C

last: Zarnescu

state: AZ

address: 1007 E Lowell St LSS 514

department: Molecular and Cellular Biology

institute: University of Arizona

organism: Drosophila melanogaster

technology: spotted oligonucleotide

distribution: custom-commercial


title: Illumina HiSeq 2500 (Huperzia drummondii)

organism: Phylloglossum drummondii


title: [Soybean] Affymetrix Soybean Genome Array

status: Public on Nov 28 2006

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Glycine max

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

The GeneChip® Soybean Genome Array can be used to study gene expression of over 37,500 soybean (Glycine max) transcripts. The array also contains transcripts for studying two pathogens important for soybean research. Specifically, the array includes probe sets to detect approximately 15,800 transcripts for Phytophthora sojae (a water mold that commonly attacks soybean crops) as well as 7,500 Heterodera glycines (cyst nematode pathogen) transcripts.

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: LC Sciences MRA-1003_miRRat_18

status: Public on Nov 29 2016

city: Chicago

first: Subhash

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

organism: Rattus norvegicus

manufacture_protocol: See manufacturer's website


title: UniversityPadova_Pecten maximus_8x60K

status: Public on Feb 05 2017

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: Pecten maximus

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


title: RayBio Human Cytokine Array C1

status: Public on Nov 21 2016

city: Taipei City

first: Pei-Yu

last: Wu

address: 128 Academia Road, Section 2, Nankang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

organism: Homo sapiens

technology: antibody

manufacture_protocol: See manufacturer's website (http://www.raybiotech.com/c-series-human-cytokine-array-1-2.html)


title: TaqMan® Human MicroRNA Arrays customized plates

city: Brasilia

first: Isabel

middle: Garcia

last: Sousa

state: Distrito Federal

address: Campus Universitario Darcy Ribeiro

department: Cell Biology

country: Brazil

institute: Univerty of Brasilia

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: HIV genotyping DNA microarray CAB-HIV-160-v4.0

city: Torrejón de Ardoz

first: Carlos

last: Briones

state: Madrid

address: Ctra de Torrejón a Ajalvir, km 4

department: Department of Molecular Evolution

country: Spain

organism: Simian-Human immunodeficiency virus

distribution: non-commercial

manufacturer: Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA)

manufacture_protocol: Each oligonucleotide (whose name corresponded to the queried HIV-1 codon) included a 'C6 amino linker' group [NH2(CH2)6] at its 5'-end, a 15-mer spacer region with either (T) 15 or (TCC)5 sequence and the specific, 13 to 17 nt-long sequence containing the queried codon at its central position.  A total of 160 different probes were synthesized and HPLC-purified (Sigma): 154 probes specific to the queried HIV-1 codons, 4 positive controls and 2 negative controls. Among the specific probes, 37 of them corresponded to different variants of 11 PR codons, while 117 covered variants of 31 RT codons including insertions and deletions in the region 67-70 as well as the multidrug complex associated to the mutation Q151M. All oligonucleotides were diluted in 1× spotting solution (Telechem-Arrayit) at 50 uM final concentration, and spotted onto super-epoxy-coated glass slides (Telechem-Arrayit). Spots containing spotting solution with no oligonucleotide were used as additional negative controls. Microarrays were printed using a GMS 417 Arrayer (Genetic Microsystems) and defined four grids or subarrays per slide. Each subarray contained 360 spots arranged in two regions (PR and RT), every oligonucleotide being printed in duplicate spots of 150 um in diameter, with a center-to- center distance of 250 um.


title: Agilent-037209 RIKEN_AT_sORF1110

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

country: Japan

institute: Kyushu Institute Technology

organism: Arabidopsis thaliana

description:
Arrays of this design have barcodes that begin with 16037209 or 2537209.

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-054269 8x60K_O.sativa_ssp_Japonica_exp-val_07-2013 (Probe name version)

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

organism: Oryza sativa Japonica Group

description: The provided SEQUENCE is only a subset of at least 30 nucleotides of the sequence in the design (this is a kind of copy protection).


title: Illumina HumanHT-12 WG-DASL V4.0 expression beadchip (gene summary, GenomeStudio report)

city: Duarte

first: Susan

last: Neuhausen

state: California

address: 1500 E duarte road

department: Population Sciences

institute: City of hope

technology: oligonucleotide beads


title: Illumina HiSeq 2500 (Carassius gibelio)

organism: Carassius gibelio


title: Illumina HiSeq 2500 (Scheffersomyces stipitis)

organism: Scheffersomyces stipitis


title: Illumina HiSeq 4000 (Nesidiocoris tenuis)

organism: Nesidiocoris tenuis


title: Agilent-069050 bacteria_mRNA_3627_Gramella flava [Probe name version]

status: Public on Nov 19 2016

city: Xiamen

first: Kai

last: Tang

address: Zhourong quan BLV 3-313, Xiamen University, Xianan, Xiamen

country: China

institute: Xiamen University

organism: Christiangramia flava

description:
3627

Arrays of this design have barcodes that begin with 16069050 or 2569050.


title: Illumina HiSeq 1500 (Acinetobacter baumannii)

organism: Acinetobacter baumannii


title: Agilent-034592 Arabidopsis thaliana PSC_Custom [Feature number version]

status: Public on Nov 27 2016

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
Arrays of this design have barcodes that begin with 16034592 or 2534592.
The ID column represents the Agilent Feature Extraction feature number.


title: Illumina HiSeq 4000 (Kluyveromyces lactis)

organism: Kluyveromyces lactis


title: Illumina HiSeq 2500 (Komagataella pastoris)

organism: Komagataella pastoris


title: Illumina HiSeq 2500 (Citrus limon)

status: Public on Nov 28 2016

organism: Citrus x limon


title: NimbleGen Human 2.0M CHARM array [Feinberg_HG18_Me_HX1]

status: Public on Nov 24 2016

city: Solna

first: David

last: Gomez-Cabrero

state: Stockholm

address: Karolinska University Hospital Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

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


title: Illumina HiSeq 4000 (Saccharomyces bayanus)

organism: Saccharomyces bayanus


title: Affymetrix Axiom® Rye600k Genotyping Array

status: Public on Nov 23 2016

city: Freising

first: Eva

last: Bauer

address: Liesel-Beckmann-Str. 2

department: Plant Breeding

country: Germany

institute: Technical University of Munich

organism: Secale cereale

description:
We generated comprehensive whole-genome shotgun (WGS) sequence data from rye inbred line Lo7 to generate the first rye genome assembly (Lo7_v2) and resequenced a panel of ten diverse rye inbred lines and Secale vavilovii for exploring genome diversity. We discovered more than 90 million single nucleotide variants (SNVs) in the rye genome and developed a high-density genotyping array to experimentally validate more than 600k SNVs (SNPs and short indels). A high-density genetic map comprising ~88k markers enabled genetic anchoring of ~44k Lo7 WGS contigs along the rye genome. Detailed information is available in the associated publication.
The original array contained 600,843 SNVs. 590,593 SNVs were developed from Lo7 WGS contigs. 2285 SNVs were taken from a previously developed custom Rye5k Illumina genotyping array based on a rye EST assembly Sce_Assembly02 (PMID: 21951788). 7,965 proprietary SNPs are omitted in this platform description.
The development and applications of the array are described in more detail in the following publication:
Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön C-C, Scholz U (2016) Towards a whole-genome sequence for rye (Secale cereale L.). Plant J (accepted)

first: Chris-Carolin

last: Schön

first: Thomas

last: Schmutzer

first: Uwe

last: Scholz

first: Viktor

last: Korzun

first: Malthe

last: Schmidt


title: Illumina HiSeq 4000 (Saccharomyces mikatae)

last: GEO

organism: Saccharomyces mikatae


title: Illumina HiSeq 2500 (Vibrio cholerae O1 biovar El Tor)

organism: Vibrio cholerae O1 biovar El Tor


title: Illumina MiSeq (Oryza sativa Japonica Group)


title: Illumina HiSeq 2500 (Sciaenops ocellatus)

organism: Sciaenops ocellatus


title: Illumina HiSeq 2500 (Sinorhizobium meliloti)

organism: Sinorhizobium meliloti


title: SABiosciences custom panel CAPH11327E

first: Christopher

last: Hourigan

address: 10 Center Drive

institute: NHLBI

organism: Homo sapiens

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Phenotypic, genomic and transcriptional analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance

city: MEXICO DISTRITO FEDERAL

first: Rosa Maria

middle: Gutierrez

last: Rios

state: DISTRITO FEDERAL

address: AV. UNIVERSIDAD 3000, UNAM, CU

department: Molecular Microbiology

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

manufacture_protocol: ss-DNA is synthesized in situ on glass substrates functionalized with amines. The synthesis process is proprietary but uses digital micromirror mediated photolithography to generate sufficient acid locally to remove acid labile protecting groups on 5'-terminal phosphoramidite monomers where the next phosphoramidite base will be coupled. The arrays can be used to hybridize cRNA or cDNA. More details in the company web page http://www.mycroarray.com/mycroarray/cat_arrays.php?org=bacteria_TZ


title: Illumina HiSeq 2000 (Atriplex prostrata x Atriplex rosea)

status: Public on Nov 16 2016

organism: Atriplex prostrata x Atriplex rosea


title: Illumina HiSeq 3000 (Atriplex prostrata x Atriplex rosea)


title: Illumina HiSeq 2000 (Atriplex prostrata)

organism: Atriplex prostrata


title: Illumina HiSeq 2000 (Atriplex rosea)

organism: Atriplex rosea


title: Illumina HiSeq 2500 (Fusarium graminearum PH-1)

status: Public on Nov 15 2016

organism: Fusarium graminearum PH-1


title: Agilent-065539 SurePrint G3 Human Custom CGH 60K array

status: Public on Nov 17 2016

city: Kuala Lumpur

first: Rosnah Binti

last: Zain

state: Kuala Lumpur

address: Jalan Lembah Pantai

department: Faculty of Dentistry

country: Malaysia

institute: University of Malaya


title: Illumina HiSeq 2000 (Herdmania momus)

status: Public on Nov 14 2016

organism: Herdmania momus


title: Illumina HiSeq 4000 (Saccharomyces cerevisiae BY4741)

organism: Saccharomyces cerevisiae BY4741


title: Illumina HiSeq 2500 (Canis lupus familiaris; Mus musculus)

organism:
Canis lupus familiaris
Mus musculus


title: DGC Drosophila v1 6k array

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

institute: Humboldt University Berlin

organism: Drosophila melanogaster

technology: spotted DNA/cDNA

manufacture_protocol: Spotted cDNA microarrays were produced essentially as  described in Klebes et al., 2002 and DeRisi et al., 1997. In brief, the Drosophila Gene Collection  (DGC 1.0, kindly provided by the Berkeley Drosophila  Genome Project) of 5,849 nonredundant cDNAs was amplified  using universal primers essentially as described at Berkeley Drosophila Genome Project resources [http://www.fruitfly.org/about/methods/ampUniGene.html].   The amplification products were purified with 96-well  format Qiagen PCR purification columns. All PCR products  were analyzed on agarose gels, and reactions with no  detectable product, multiple bands or bands of unexpected  size were repeated using Herculase (Amersham) or Expand  polymerase (Roche). One hundred and seventy-five cDNAs  from our lab collection were amplified and added to the set,  resulting in a total of 6,024 cDNAs. Reactions were arrayed  into 384-well plates and printed on poly-L-lysine-coated  glass slides using a linear servo arrayer and ArrayMaker  Version 2 control software. To minimize background caused  by oxidation of the polylysine coating, slides were pretreated  by a protocol suggested by Paul Ebert. Before post-processing,  slides were incubated for 5 min in 3x SSC; 0.2% SDS at  65°C, washed first in water and then in 95% ethanol, followed by centrifugation to dry the slides. Slides were then treated, and the hybridization reaction was carried out as described at Drosophila Genome Project resources [http://www.fruitfly.org/about/methods/ampUniGene.html]. We indirectly labeled the hybridization probes by incorporation of amino-allyl modified nucleotides in a first-strand cDNA RT reaction. Monofunctional Cy5 or Cy3 dye (Amersham) was subsequently coupled to the reactive residues. Multiple hybridizations were carried out, and dye labeling was reversed to avoid systematic bias.


title: Illumina HiSeq 2000 (Balanoglossus misakiensis)

organism: Balanoglossus misakiensis


title: Illumina HiSeq 2000 (Acropora)

organism: Acropora


title: Illumina HiSeq 2000 (Haliotis asinina)

organism: Haliotis asinina


title: Illumina HiSeq 2000 (Dama dama)

organism: Dama dama


title: Agilent-033126 FMDsero3_3222011

status: Public on Nov 10 2016

city: Greenport

first: Roger

middle: William

last: Barrette

state: NY

address: Plum Island Animal Disease Center

department: Diagnostic Services

institute: USDA/APHIS/FADDL

organism: Foot-and-mouth disease virus

description:
Arrays of this design have barcodes that begin with 16033126 or 2533126.

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 MiniSeq (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Illumina HiSeq 2000 (Bambusa vulgaris)

organism: Bambusa vulgaris


title: Illumina HiSeq 2000 (Ailuropoda melanoleuca)

organism: Ailuropoda melanoleuca


title: Exiqon Human PCR panels I+II, V1.R (miRBase version 12)

status: Public on Nov 11 2016

city: Hannover

first: Julia

last: Osipova

address: Carl-Neuberg Str. 1

department: IMTTS

institute: MHH

organism: Homo sapiens

description: PCR assay


title: Illumina NextSeq 500 (Staphylococcus aureus subsp. aureus USA300)

status: Public on Nov 13 2016


title: Geochip 5.0

status: Public on Nov 09 2016

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

organism:
Bacteria
Archaea
Eukaryota
Viruses


title: NimbleGen Peanut oligonucleotide microarray (36,741)

city: Qingdao

last: Chen

address: wannianquan road

institute: Shandong Peanut Research Institute

organism: Arachis hypogaea

description: A 72 K format micorarray was designed for 36,741 unigenes assembled from publicly available and  inhouse ETSs. Each unigene has two probes.

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


title: Illumina HiSeq 2500 (Patiria miniata)

organism: Patiria miniata


title: EuroGenTec Calbicans 7K

status: Public on Nov 18 2016

city: Jena

first: Sebastian

last: Vlaic

address: Beutenbergstr. 11a

department: Systems Biology and Bioinformatics

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute -

organism: Candida albicans

manufacture_protocol: 60mer Oligos were spotted in duplicates


title: HumanOmniExpress-24 v1.1 BeadChip [SNP_ID version]

last: admin


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]

status: Public on Jan 18 2011

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
HuGene-1_1-st-v1.na32.hg19.transcript.csv
#%create_date=Tue Jun 21 17:41:46 2011 PDT
#%chip_type=HuGene-1_1-st-v1
#%lib_set_name=HuGene-1_1-st
#%lib_set_version=v1
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Homo sapiens
#%genome-lifted_from-version-ucsc=hg18
#%genome-lifted_from-version-ncbi=36.1
#%netaffx-annotation-date=2011-06-22
#%netaffx-annotation-netaffx-build=32

relation: Alternative to: GPL15640 (Alternative CDF)

relation: Alternative to: GPL18190 (Alternative CDF [HuGene11stv1_Hs_ENTREZG_15.1.0])

relation: Alternative to: GPL16977 (Alternative CDF)

relation: Alternative to: GPL20234 (alternative CDF [HuGene11stv1_Hs_ENSG version 18.0.0])

relation: Alternative to: GPL20880 (alternative CDF [HuGene11st_Hs_ENTREZG_18.0.0])

relation: Alternative to: GPL22286 (alternative CDF [HuGene11stv1_Hs_ENSG version 19.0.0])

relation: Alternative to: GPL22654 (alternative CDF [HuGene11stv1_Hs_ENTREZG version 15.1.0]))


title: Agilent-084171 Mus musculus 8x60k CGH 0mGyS G4125A CGH array

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16084171 or 2584171

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: Custom panel of 81 Taqman probes

city: Pittsburgh

first: Guang

last: Li

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

description: PCR assay


title: Illumina HiSeq 2000 (Ophiorrhiza pumila)

organism: Ophiorrhiza pumila


title: Illumina NextSeq 500 (Trichomonas vaginalis)

status: Public on Nov 08 2016

organism: Trichomonas vaginalis


title: Ion Torrent Proton (Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819)


title: Illumina HiSeq 2000 (Xanthomonas oryzae pv. oryzae KACC 10331)


title: Ion Torrent Proton (Campylobacter jejuni subsp. jejuni F38011)


title: Ion Torrent Proton (Campylobacter jejuni subsp. jejuni 81-176)


title: [ADXOCv1a520630] Almac Ovarian Cancer Disease Specific Array (DSA) ™

city: Belfast

first: Jaine

last: Blayney

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queen's University


title: Illumina HiSeq 4000 (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Agilent-084172 Mus musculus 8x60k 0mGyT G4125A CGH array

description:
Arrays of this design have barcodes that begin with 16084172 or 2584172

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-076323 En2_2 Custom Tiling Array G4822A (Feature number version)

status: Public on Nov 04 2016

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

description:
Arrays of this design have barcodes that begin with 16076323 or 2576323

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: Applied Biosystems microfluidic cards qunatitative PCR [catalog 4367563]

status: Public on Nov 07 2016

city: Nijmegen

first: Niccolo

last: Mariani

address: Geert Grooteplein Zuid 8

country: Netherlands

institute: Radboudumc

description:
real-time quantitative PCR on microfluidic card
customizable card


title: Agilent-055693 Arraystar Mouse LncRNA microarray V3A (Probe Name version)

status: Public on Nov 05 2016

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

description: Arraystar Mouse LncRNA Microarray V3.0 is designed for the global profiling of mouse lncRNAs and protein-coding transcripts, which is updated from the previous Microarray V2.0. About 35,923 lncRNAs and 24,881 coding transcripts can be detected by our third-generation lncRNA microarray. The lncRNAs are carefully constructed using the most highly-respected public transcriptome databases (RefSeq, UCSC knowngenes, Ensembl, etc.), as well as landmark publications. Each transcript is represented by a specific exon or splice junction probe which can identify individual transcripts 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 MiSeq (Propionibacterium freudenreichii)

last: GEO

organism: Propionibacterium freudenreichii


title: Illumina HiSeq 2000 (Xiphophorus multilineatus)

organism: Xiphophorus multilineatus


title: Illumina MiSeq (Escherichia coli O25b:H4-ST131)

status: Public on Nov 03 2016

organism: Escherichia coli O25b:H4-ST131


title: Illumina HiSeq 2000 (Acaryochloris marina MBIC11017)

status: Public on Nov 01 2016

organism: Acaryochloris marina MBIC11017


title: Illumina HiSeq 2000 (Fusarium fujikuroi)

organism: Fusarium fujikuroi


title: Agilent Custom Xanthomonas campestris 8x15K Array designed by Genotypic Technology Private Limited. (AMADID: 28737)

status: Public on Nov 02 2016

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: Xanthomonas campestris pv. campestris str. 8004


title: NimbleGen Custom Eukaryotic Gene Expression 385K Array (5224667), Medaka (Oryzias latipes), Design ID: RDKK097

city: Seattle

first: Yasushi

last: Shibata

state: Washington

address: 1122 NE Boat Street

department: SAFS

institute: University of Washington

organism: Oryzias latipes

description: Species: Oryzias latipes; Data Source; ; Database site TIGR; Database name TIGR Medaka Gene Index; Version/Revision Release 6.0; URL http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=o_latipes; Released date June 17, 2006; Type of array: Eukaryotic Expression(4plex); Number of target: 63,698; Length of probes: 60 mer; Number of probes per target: 6 pair; Density: 1 in 2; Replicate: 1; Total number of probes: 380,766; Cutoff value: 1000; Roche's design ID: RDKK097; Design file name: 2008-08-18_RDKK097_Olat_60mer_expr; Notice:; We set 7,000 random probes to fill empty spots.; Part of targets are customer original.

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


title: Lampe Lab Custom Antibody Array [SA10]

first: Paul

last: Lampe

state: WA

address: 1100 Fairview Ave. N., Mail Stop M5-C800

institute: Fred Hutchinson Cancer Research Center

manufacture_protocol: See previous publication (PMCID: PMC2671017)


title: Lampe Lab Custom Antibody Array [SA9]


title: Lampe Lab Custom Antibody Array [SA7]


title: NimbleGen-Zebrafish-135k-UvA-v1.0

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

institute: University of Amsterdam

organism: Danio rerio

description:
NimbleGen design name 100922;  A zebrafish 60 mer array (Zv9) containing probesets of up to 3 probes (numbered 1, 2, and 3 from the 3' end forward). See:  doi:10.1186/1756-0500-3-192. The design includes 5,000 negative control probes (NC), 5,000 Spatial Control probes (SC), 1,300 Concentration Control probes (CC) and 6,545 Amplification Control (AC) probes; AC_PM probes are designed to perfectly match the spiked-in molecule, AC_MM probes have a number of mismatches to the spiked-in molecule indicated by a number following '_mm_'.
100922_DanioRerio_FW_EXP.ndf
100922_DanioRerio_FW_EXP_HX12.ncd

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology.


title: Streptococcus pneumoniae D39 Agilent-065256

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

organism: Streptococcus pneumoniae D39

description:
Streptococcus pneumoniae D39
Including rRNA and tRNA


title: Lampe Lab Custom Antibody Array [SA4]

organism: Homo sapiens


title: Agilent-024764 1MKGB 1x1M CGH array [Probe Name version]

status: Public on Jul 27 2016

description:
Agilent-024764 1MKGB

The ID column represents the Agilent Probe Names.
**A different version of this platform with the Agilent Feature Extraction feature numbe in the ID column is assigned accession number GPL22341.

Arrays of this design have barcodes that begin with 16024764 or 2524764.


title: Illumina Infinium Human CytoSNP FFPE-12v2.1 arrays

status: Public on Jul 01 2013

city: Brisbane

first: Peter

last: Simpson

address: Royal Brisbane & Women's Hospital

department: UQ Centre for Clinical Research

country: Australia

institute: The University of Queensland


title: NanoString Human miRNA version 3

city: Monrovia

first: Claude

middle: J

last: Rogers

state: CA

address: 1225 S. Shamrock Ave.

institute: ChromoLogic

technology: other


title: CATMA Arabidopsis V4 TAIR V9 spotted cDNA array

status: Public on Oct 03 2012

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

organism: Arabidopsis thaliana

description: The Hp* probes are probes designed against the pathogen Hyaloperonospora arabidopsidis (previously peronospora).

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


title: Illumina HumanHap550 Genotyping BeadChip v3

status: Public on Feb 05 2008

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Version 3, Illumina Sentrix HumanHap550 Genotyping BeadChip

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


title: Illumina HiSeq 2000 (Pestalotiopsis fici)

organism: Pestalotiopsis fici


title: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: htmg430pmmmentrezgaltrabio131772]

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

description: This is an alternative CDF.

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

manufacture_protocol: see manufacturer's web site


title: Agilent-024764 Mus musculus 1x1M CGH array [Feature Number version]

status: Public on Aug 19 2016

last: OGURA

description:
Arrays of this design have barcodes that begin with 16024764 or 2524764.

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.
**A different version of this platform with the Agilent Probe Names in the ID column is assigned accession number GPL22176.

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.

Please note that the ROW/COL information (for a given probe) is different between the platform file (024764_D_GEO_20160810.txt) and the associated sample raw data files, and both are included in the platform table.


title: Illumina HiSeq 2500 (Canis lupus familiaris)

status: Public on Oct 05 2015

country: USA

organism: Canis lupus familiaris


title: Agilent-034592 Arabidopsis thaliana PSC_Custom

status: Public on Jul 13 2015

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

description: the probes were designed based on expressed genes and transcripts of TAIR 10 genome using previous tiling-array and RNA-seq analyses (Kawaguchi et al. 2012; Matsui et al. 2008; Okamoto et al. 2010).