title: Agilent-067406 CBC lncRNA+mRNA microarray V3.0 (lncRNA version)

status: Public on Nov 29 2017

city: Hangzhou

first: Qiuli

last: FU

state: Zhejiang

address: Jiefang road 88#

country: China

institute: Zhejiang University

organism: Homo sapiens

technology: in situ oligonucleotide

description: Agilent SurePrint G3

distribution: custom-commercial


title: Illumina MiSeq (Corynebacterium diphtheriae NCTC 13129)

status: Public on Apr 25 2017

last: GEO

country: USA

organism: Corynebacterium diphtheriae NCTC 13129

technology: high-throughput sequencing

distribution: virtual


title: Affymetrix Saccharomyces cerevisiae TAG4 101K array [GenFlex_Tag_16K_v2]

status: Public on Apr 30 2017

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

organism: Saccharomyces cerevisiae

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


title: AB SOLiD System (Oryza sativa Japonica Group)

status: Public on Apr 28 2017

organism: Oryza sativa Japonica Group


title: Illumina HiSeq 2000 (Chaetomium thermophilum; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Thermochaetoides thermophila


title: Illumina HiSeq 4000 (Ostrea lurida)

organism: Ostrea lurida


title: Agilent-050749 JiangdouExpr

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

organism: Vigna unguiculata

description:
Arrays of this design have barcodes that begin with 16050749 or 2550749.

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: Ion Torrent Proton (Pseudomonas aeruginosa)

organism: Pseudomonas aeruginosa


title: [Glyco_v4_Hs] Custom Affymetrix Glyco v4 GeneChip

status: Public on Oct 23 2010

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description:
The Glyco v4 array was designed in 2008 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species.

This array also includes "GC bin" probes (100 for each bin) for use in background correction. These probes are used as an alternative to the PM/MM-based background correction methods. Mismatch probes are not used on this array.

There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file.  The human CDF file is named: "GLYCOv4_Hs" and the mouse CDF file is named: "GLYCOv4_Mm".

Probeset design: The v4 array uses 25 probes to target the first 600 bases from 3' end of each transcript. This region is called Probe Set Region 1 indicated by a psr1 in the probe set name. Up to 4 additional sets of  5 probes are used to target the transcript in 280 base increments upstream (towards the 5' end of the transcript) from the first 600 base region. These are indicated as psr2, psr3 and psr4 in the probeset name. If no psr appears in the probe set name, this indicates that probes are targeting Probe Set Region 1 and that no additional probe sets were designed upstream (towards the 5' end of the transcript) for this transcript accession. Generally only data from Probe Set Region 1 are shown. Data from psr2-4 is generally ignored. All probes are for antisense target and may include a suffix of "_s", "_x" consistent with Affymetrix probe design algorithms used for all commercial Affymetrix 3' arrays.

manufacture_protocol: see manufacturer's web site


title: Agilent-027375 Sheepshead minnow SHM 15K

status: Public on Apr 29 2017

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

department: Biology

institute: Francis Marion University

organism: Cyprinodon variegatus

description:
Sheepshead minnow (Cyprinodon variegatus)

Arrays of this design have barcodes that begin with 16027375 or 2527375.

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 4000 (Mauremys reevesii)

status: Public on Apr 26 2017

organism: Mauremys reevesii


title: Illumina HiSeq 2000 (Bordetella pertussis)

organism: Bordetella pertussis


title: Illumina HiSeq 2500 (Gerbera delavayi)

organism: Gerbera delavayi


title: Agilent-069114 Human 8x60K Microarray (Feature Number version)

status: Public on Apr 27 2017

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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


title: Illumina HiSeq 2500 (Populus davidiana)

organism: Populus davidiana


title: Illumina HiSeq 2500 (Tetranychus urticae)

organism: Tetranychus urticae


title: Illumina HiSeq 2500 (Homo sapiens; Sphinx1.76-related DNA)

organism:
Homo sapiens
Sphinx1.76-related DNA


title: Illumina HiSeq 2500 (Saccharomyces cerevisiae S288C)

organism: Saccharomyces cerevisiae S288C


title: Ion Torrent Proton (Bacillus mycoides)

organism: Bacillus mycoides


title: Illumina HiSeq 2500 (Toxoplasma gondii)

organism: Toxoplasma gondii


title: Illumina HiSeq 2500 (Homo sapiens; Human gammaherpesvirus 4; Human gammaherpesvirus 8)

status: Public on Apr 24 2017

organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8


title: Illumina HiSeq 2500 (Homo sapiens; Human papillomavirus type 31)

organism:
Homo sapiens
human papillomavirus 31


title: Illumina NextSeq 500 (Human gammaherpesvirus 8)

organism: Human gammaherpesvirus 8


title: [RaGene-2_1-st] Affymetrix Rat Gene 2.1 ST Array [Brainarray ENTREZG Version 19]

organism: Rattus norvegicus

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
Identical to GPL19271 but uses a custom CDF: ragene21st_Rn_ENTREZG.cdf

relation: Alternative to: GPL19271 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Agilent-076115 maize 4x44K Microarray (Feature number version)

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

organism: Zea mays

description: Zea mays (B73)


title: Illumina HiSeq 2000 (Panax notoginseng)

organism: Panax notoginseng


title: Illumina HiSeq 4000 (Homo sapiens; Human gammaherpesvirus 4)

organism:
Homo sapiens
human gammaherpesvirus 4


title: Illumina HiSeq 2500 (Burkholderia sp. b13)

organism: Burkholderia sp. b13


title: Illumina HiSeq 2500 (Burkholderia sp. b13; Rhizopus microsporus ATCC 52813)

organism:
Rhizopus microsporus ATCC 52813
Burkholderia sp. b13


title: Illumina HiSeq 2500 (Rhizopus microsporus ATCC 52813)

organism: Rhizopus microsporus ATCC 52813


title: Illumina HiSeq 2500 (Ralstonia solanacearum)

status: Public on Apr 21 2017

organism: Ralstonia solanacearum


title: Toll-like Receptor RT2 Profiler PCR Array panel

city: Thessaloniki

first: Nikolaos

last: Zogas

address: Exokhi

department: Hematology-BMT Unit

country: Greece

institute: George Papanicolaou Hospital

organism: Mus musculus

technology: RT-PCR

description:
PCR assay
Qiagen RT² Profiler panel of PCR assays (96-well plate).

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2500 (Cucumis melo var. cantalupo)

organism: Cucumis melo var. cantalupo


title: AB SOLiD System (Drosophila simulans)

status: Public on Apr 20 2017

organism: Drosophila simulans


title: Illumina Genome Analyzer II (Drosophila grimshawi)

organism: Drosophila grimshawi


title: Illumina Genome Analyzer II (Drosophila persimilis)

organism: Drosophila persimilis


title: PacBio RS II (Lilium maculatum)

status: Public on Apr 19 2017

organism: Lilium maculatum


title: Illumina HiSeq 2500 (Lilium maculatum)


title: Illumina HiSeq 2500 (Streptococcus pyogenes serotype M3)

status: Public on Apr 18 2017

organism: Streptococcus pyogenes serotype M3


title: CSIR-CDRI - TaqMan Human miRNA array (miRBase v. 21)

city: Lucknow

first: Dr. Bhupendra

middle: Narain

last: Singh

state: Uttar Pradesh

address: Jankipuram Extension, Sec.-10, Sitapur Road

department: Microbiology

country: India

institute: CSIR-CDRI Lucknow

organism: Homo sapiens

description:
Real time PCR assay
TLDA


title: Illumina HiSeq 2500 (Streptococcus pyogenes serotype M1)

organism: Streptococcus pyogenes serotype M1


title: Agilent-026435 Mouse miRNA Microarray (miRBase Release 14, miRNA ID version)

description: Grid Date: 12/2/2009 (corresponding to miRBase release 14)


title: [PrimeView] Affymetrix Human Gene Expression Array [Brainarray ENTREZG Version 18]

description: This is identical to GPL15207 but a custom CDF environment was used to extract data [Brainarray (version 18)].

relation: Alternative to: GPL15207 (Alternative CDF [official])

manufacture_protocol: See details from Affymetrix.


title: Illumina HiSeq 2000 (Drosophila persimilis)


title: Custom NimbleGen 12-plex Bufo marinus, Bufo boreas, Xenopus tropicalis Oligo Expression Array

city: Berkeley

first: Thomas

last: Poorten

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

organism:
Xenopus tropicalis
Rhinella marina
Anaxyrus boreas

description: The custom Nimblegen microarray design included 135,200 60-bp probes (excluding control probes) targeting 31,367 transcript contigs from Bufo marinus, Bufo boreas, and model species Xenopus tropicalis, with 4 probes per probe-set. Probe-sets were defined as all probes that mapped to a single transcript. We used the 12-plex microarray platform (12 arrays per glass slide). Annotation was performed using the blat program to identify Bufo contigs with high sequence identity to X. tropicalis transcripts (Ensembl assembly v4.2). We ran blat with translated Bufo contigs and translated X. tropicalis transcripts (parameters: -q=dnax –t=dnax) in order to find orthologous sequences at the protein level, which is more conserved between divergent species. We parsed blat hits to remove short hits (<100 bp aligned to query) and low scoring hits (Expectation value >1.0e-12). We used the Ensembl Gene Identifier (e.g. ENSXETG00000XXXXXX) for the blat hit with longest alignment to the query as the final annotation call. We then imported annotation metadata with the biomart.org pipeline: Ensembl gene name and description, Gene Ontology (GO) terms, Ensembl protein families, Interpro protein domains. Next, we used the blast2go pipeline to annotate Bufo contigs without GO term metadata (6328 contigs). We used the blastx method with the NCBI nonredundant protein database to identify blast hits, and proceeded with blast2go pipeline with default settings.

manufacture_protocol: See manufacturer's website


title: Exiqon miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (miRBase v18.0)

status: Public on Apr 17 2017

city: Beijing

first: SHUAI

last: HUANG

address: Nanwei Road NO2

institute: Institute of Materia Medica,Chinese Academy of Medical Sciences/Peking Union Medical College

technology: spotted oligonucleotide

description:
Product=miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno
ProductDate=March 2012
ProductNumber=208500,208501,208502,208510,208520,208521,208522
LotNumberRange=35106-35106
GalFileCreationDate=2014-07-02 10:54
ArrayContents_DesignedFor=miRBase 18.0
ArrayContents_CurrentNameColumn=miRBase 21.0

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


title: Illumina MiSeq (1,4-dioxane degrading enrichment culture)


title: PacBio RS II (Human alphaherpesvirus 1)

status: Public on Apr 14 2017

organism: Human alphaherpesvirus 1


title: Agilent-081421 Horse_60K_2016_01_22 021322

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

organism: Equus caballus

description:
Arrays of this design have barcodes that begin with 16081421 or 2581421.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Illumina HiSeq 2000 (coral metagenome)

organism: coral metagenome


title: Multi-species Autoantigen Microarray 94

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted peptide or protein

distribution: non-commercial

manufacturer: University of Texas Southwestern Medical Center

manufacture_protocol: Dilute peptides, proteins, protein complexes, or other antigens in PBS-0.1% Tween20 to 0.1 - 0.2 mg/mL.  Transfer diluted antigens transferred to 384-well print plates (15 μL/well). Antibody or other proteins/peptides prelabeled with Cy-3 and / or Cy-5 (diluted to 0.1 μg/μL) can be added to the print plate to serve as marker spots to orient the arrays post-scanning.  Using a biorobotic arrayer (MicroGrid 610) and quill pins (Genomic Solution) to print antigens on nitrocellulose coated microarray slides (FAST Slide, 16 pad, Whatman Inc). Slides were kept at 75% humidity chamber for 12 hours.  Store arrays at 4°in slide boxes sealed in plastic heat-sealable pouches. Reactivity is generally best within 1 month of printing, but printed antigens can retain reactivity for months.


title: nCounter GX Mouse Inflammation Kit (Nanostring Technologies)

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

technology: other

description: Digital molecular barcoding

distribution: commercial


title: NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100205_HG18_Promoter_MeDIP_HX1]

status: Public on Apr 13 2017

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen Street

institute: University of Arizona

description:
Design ID: 11333
Design name: 100205_HG18_Promoter_MeDIP_HX1
Genome build: HG18

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


title: NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100718_HG18_Promoter_MeDIP_HX1]

description:
Design ID: 537423
Design name: 100718_HG18_Promoter_MeDIP_HX1
Genome build: HG18


title: Agilent-020871 Eucommia ulmoides Eul_4x44K_A

city: Suita

first: Yoshihisa

last: Nakazawa

state: Osaka

address: 8, Yamadaoka-2

department: Graduate School of Engineering

country: Japan

institute: Osaka University

organism: Eucommia ulmoides

description:
Arrays of this design have barcodes that begin with 16020871 or 2520871.

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 (Pochonia chlamydosporia)

organism: Pochonia chlamydosporia


title: nCounter Mouse v.1.5 miRNA Expression Assay (Nanostring Technologies)

description: Digital molecular barcoding


title: Illumina HiSeq 2000 (Sodalis praecaptivus)

status: Public on Apr 12 2017

organism: Sodalis praecaptivus


title: Illumina HiSeq 2500 (Oryzias latipes)

organism: Oryzias latipes


title: Galbraith Lab Maize Unigene cDNA microarray slide UG1-2.2

city: Ithaca

first: Tim

middle: L.

last: Setter

state: NY

address: 517 Bradfield Hall

department: Crop & Soil Sci; Plant Breeding & Genetics

institute: Cornell University

organism: Zea mays

technology: spotted DNA/cDNA

middle: L

first: LongXi

last: Yu

manufacture_protocol: Microarray slides were printed using an OmniGridder (GeneMachines, San Carlos, California) and 8 Majer Precision pins (11077-1 Rev A MicroQuill 2000 Microarray Printing Tip, Majer Precision Engineering, Tempe, Arizona). Instrument settings were as follows: Dip time 500 milliseconds, Print time 0, After every Sample (Wash 2000ms, Dry 2000ms) 8 times, After every Plate (Sonicate 30,000ms, Wash 10,000ms, Dry 2000ms) 2 times-wash solution was 0.5 X SSC. Instrument settings were optimized prior to printing using a Cy3-labeled oligo to check print quality and verify no carryover between samples.


title: Illumina MiSeq (Streptomyces tsukubensis)

status: Public on Apr 11 2017

last: GEO

organism: Streptomyces tsukubensis


title: Illumina HiSeq 2000 (Streptomyces tsukubensis)


title: Agilent-034525 Human Keratinocyte Array [Probe Name]

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

description:
Arrays of this design have barcodes that begin with 16034525 or 2534525.
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 (Nicotiana benthamiana)

organism: Nicotiana benthamiana


title: Illumina HiSeq 2000 (Mycobacterium smegmatis)

status: Public on Apr 10 2017

organism: Mycolicibacterium smegmatis


title: HiSeq X Ten (Rhododendron simsii)

organism: Rhododendron simsii


title: Illumina HiSeq 3000 (Solanum lycopersicum)

organism: Solanum lycopersicum


title: Illumina HiSeq 2500 (Eubacterium limosum)

organism: Eubacterium limosum


title: Illumina MiSeq (Eubacterium limosum)


title: Illumina HiSeq 4000 (Deinococcus radiodurans)

organism: Deinococcus radiodurans


title: Illumina HiSeq 2000 (Morone chrysops x Morone saxatilis)

status: Public on Apr 09 2017

organism: Morone chrysops x Morone saxatilis


title: Illumina MiSeq (Callorhinchus milii)

organism: Callorhinchus milii


title: Illumina HiSeq 4000 (Camellia sinensis)

organism: Camellia sinensis


title: Agilent-075784 human circRNA Array (V1.0) 4x180K

status: Public on Apr 06 2017

city: Jinan

first: shengda

last: cao

state: Shandong Province

address: wenhua west road

department: ENT

institute: Qilu hospital

organism: Homo sapiens


title: Illumina HiSeq 1500 (Aedes aegypti)

status: Public on Apr 07 2017

organism: Aedes aegypti


title: Illumina HiSeq 2000 (Copadichromis virginalis x Mchenga conophoros)


title: Illumina HiSeq 2500 (Populus trichocarpa)

organism: Populus trichocarpa


title: Illumina Genome Analyzer II (Anolis carolinensis)

status: Public on Apr 05 2017

organism: Anolis carolinensis


title: Illumina HiSeq 2000 (Leishmania donovani)

organism: Leishmania donovani


title: Illumina HiSeq 2500 (Azotobacter vinelandii)

status: Public on Apr 04 2017

organism: Azotobacter vinelandii


title: Illumina NextSeq 500 (Setaria italica)

organism: Setaria italica


title: Illumina HiSeq 2500 (Staphylococcus epidermidis)

organism: Staphylococcus epidermidis


title: Illumina HiSeq 2500 (Ornithorhynchus anatinus)

organism: Ornithorhynchus anatinus


title: Agilent-084146 Clostridium carboxidivorans

city: Bunkyo-ku

first: Tatsuya

last: Inoue

state: Tokyo

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

organism: Clostridium carboxidivorans

description:
Arrays of this design have barcodes that begin with 16084146 or 2584146.

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 (Pseudoalteromonas sp. SCSIO_11900)

status: Public on Apr 03 2017

organism: Pseudoalteromonas sp. SCSIO_11900


title: Illumina HiSeq 2500 (Anolis carolinensis)


title: Illumina HiSeq 2000 (Streptococcus sanguinis SK36)

organism: Streptococcus sanguinis SK36


title: Illumina Human Sentrix-8 Array (2010)

status: Public on Apr 01 2017

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

country: Germany

institute: Rottal-Inn Kliniken KU

technology: oligonucleotide beads


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v21]

first: GEO

last: admin

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment.

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


title: Fusarium fujikuroi annotation version 2 gene expression array [121227_Ffuji_v2_2_BT]

city: Neuherberg, Germany

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

organism: Fusarium fujikuroi

description: NimbleGen design name 121227_Ffuji_v2_2_BT_expr

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


title: Illumina HiSeq 2500 (Trypanosoma brucei brucei)

status: Public on Mar 31 2016

organism: Trypanosoma brucei brucei


title: Illumina NextSeq 500 (Brachypodium distachyon)

organism: Brachypodium distachyon


title: Illumina MiSeq (Saccharomyces cerevisiae S288c)

status: Public on Apr 19 2015

organism: Saccharomyces cerevisiae S288C


title: EmbryoGENE DNA Methylation Array Bovine 2x400K v2.0 (Feature Number)

status: Public on Sep 09 2014

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

organism: Bos taurus


title: Agilent-079011 human circRNA Array (V1.0) 4x180K

organism: Homo sapiens


title: Agilent-029634 Brassica napus 60K v1.0 FUB (EST)

status: Public on Jan 15 2015

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

institute: Freie Universität Berlin

organism: Brassica napus

description: GridName 029634

manufacture_protocol: see manufacturer's web site at http://www.genomics.agilent.com/article.jsp?pageId=2011


title: Agilent-066414 Daphnia magna 180k v2

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

country: Spain

institute: IDAEA-CSIC

organism: Daphnia magna

description:
Please note that the gene identifier in the accession string refers to a set of gene models generated by the Daphnia magna Genome consortium;
http://server7.wfleabase.org/prerelease3/Daphnia_magna/gene-predictions/daphmagna_201208a9/
however, they are not yet publicly available as of this moment.

The '066414_180K_annotation.xlsx' file contains a full annotation of these gene models, by BLAST to several databases, REFSEQ, Flybase, Swissprot.

The 'daphnia_magna_gene_models_finals_fasta' file contains the gene name and respective sequence

Arrays of this design have barcodes that begin with 16066414 or 2566414.

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: Ion Torrent PGM (Schizosaccharomyces pombe)

status: Public on Nov 14 2016

organism: Schizosaccharomyces pombe


title: Illumina NextSeq 500 (Aspergillus fumigatus)

organism: Aspergillus fumigatus


title: Agilent-026900 Paracoccus denitrificans

status: Public on Nov 18 2013

city: Norwich

first: Matthew

middle: John

last: Sullivan

state: Norfolk

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

organism: Paracoccus denitrificans

description:
probes for ORFs from Paracoccus denitrificans PD1222. Design was aimed to have tiled probes of around 60 bp, every 100 bp throughout the genome, where possible"
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."

manufacturer: Agilent Technologies / Oxford Gene Technology


title: Nanostring nCounter Gene Expression Assay (Pan Cancer Immune Panel)

city: NEW YORK

first: Mauro

middle: Pellegrino

last: Avanzi

address: 427 east 73rd street apt 5B

institute: Memorial Sloan Kettering Cancer Center

manufacture_protocol: nCounter XT CodeSet Gene Expression  Assays, July-2016.


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

status: Public on Jan 18 2011

city: Santa Clara

last: Affymetrix

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

MoGene-1_1-st-v1.na31.mm9.transcript.csv
#%create_date=Fri Aug 27 17:50:02 2010 PDT
#%chip_type=MoGene-1_1-st-v1
#%lib_set_name=MoGene-1_1-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Mus musculus
#%genome-lifted_from-version-ucsc=mm8
#%genome-lifted_from-version-ncbi=36
#%netaffx-annotation-date=2010-07-15
#%netaffx-annotation-netaffx-build=31

relation: Alternative to: GPL17153 (Alternative CDF [MoGene11stv1_Mm_ENTREZG_15.1.0])

relation: Alternative to: GPL19138 (Alternative CDF [MoGene11stv1_Mm_ENTREZG_14.1.0])

relation: Alternative to: GPL19143 (Alternative CDF [MoGene11stv1_Mm_ENTREZG_17.0.0])

relation: Alternative to: GPL20837 (Alternative CDF [MoGene11stv1_Mm_ENTREZG_19.0.0])

relation: Alternative to: GPL23319 (transcript-level na35ens81)


title: Illumina HiSeq 3000 (Danio rerio)

organism: Danio rerio


title: Agilent-049801 Custom Mouse lncRNA 4*180K array

status: Public on Jun 09 2016

city: Changsha

first: Mei-hua

last: Bao

state: Hunan

address: No. 1501, Leifeng Road

department: Anatomy, Histology and Embryology

institute: Changsha Medical University


title: Illumina HiSeq 3000 (Drosophila melanogaster)

status: Public on Apr 19 2017

organism: Drosophila melanogaster


title: Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Feature Number version)

status: Public on Aug 13 2009

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 Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL12621


title: nCounter Mouse Immunology Panel

status: Public on Mar 31 2015

city: Seattle

first: NanoString

last: Technologies

address: 530 Fairview Ave N  |  Suite 2000

institute: NanoString Technologies

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


title: Illumina HiSeq 4000 (Bos taurus)

status: Public on Apr 12 2017