title: Agilent-064901 DrosophilaManakChip2 G4123A

status: Public on Mar 10 2020

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

country: USA

institute: University of Iowa

organism: Drosophila melanogaster

technology: in situ oligonucleotide

description: Nimblegen LiftOver Design drosophila; chip2

distribution: custom-commercial

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


title: Agilent-064928 DrosophilaManakChip1 G4123A


title: NimbleGen Arabidopsis thaliana Gene Expression 12x135K Array [100718_Athal_TAIR9_exp; gene-level]

status: Public on Apr 21 2018

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

organism: Arabidopsis thaliana

description:
designname=100718_Athal_TAIR9_exp
designid=535493

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


title: PROSTVAC a96 ver. 1

status: Public on Aug 25 2017

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

institute: National Cancer Institute

organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Sus scrofa domesticus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

technology: spotted peptide or protein

description:
Each slide contains 16 identical array containing 96 components printed in duplicate (192 features total)
spotted glycoproteins and neoglycoproteins

distribution: non-commercial

manufacturer: National Cancer Institute, Chemical Glycobiology Section

manufacture_protocol: Glycoproteins and neoglycoproteins spotted onto epoxide functionalized glass slides (ArrayIt SME2) using a MicroGrid II arrayer.


title: Illumina HiScanSQ (Acinetobacter baumannii)

status: Public on Jun 27 2017

last: GEO

organism: Acinetobacter baumannii

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2500 (Apostichopus japonicus)

status: Public on Jun 28 2017

organism: Apostichopus japonicus


title: Agilent-076005 Pseudomonas aeruginosa UCBPP-PA14 SurePrint G3 Custom Gene Expression Microarray

status: Public on Jun 29 2017

city: Seoul

first: Taek-Seung

address: Anam-ro 145

department: school of civil, Environmental & Architectural Engineering

institute: Korea University

organism: Pseudomonas aeruginosa UCBPP-PA14


title: Exiqon miRCURY LNA microRNA array, 7th generation [miRBase v18]

city: Jinan

first: Ya-Wen

last: Wang

address: Wen Hua Xi Road 107

country: China

institute: Shandong University

organism: synthetic construct

technology: spotted oligonucleotide


title: Illumina Genome Analyzer II (Vaccinium ashei)

organism: Vaccinium ashei


title: AB 5500xl Genetic Analyzer (Arabidopsis thaliana; Meloidogyne incognita)

status: Public on Jun 26 2017

organism:
Arabidopsis thaliana
Meloidogyne incognita


title: Agilent-084032 Marcanthia_V1

status: Public on Apr 09 2018

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

organism: Marchantia polymorpha

description:
Marcanthia_V1

Arrays of this design have barcodes that begin with 16084032 or 2584032.

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 (Varroa destructor)

organism: Varroa destructor


title: AB 5500xl Genetic Analyzer (Meloidogyne incognita)

organism: Meloidogyne incognita


title: Illumina HiSeq 2000 (Citrus unshiu)

organism: Citrus unshiu


title: Ion Torrent PGM (Anas platyrhynchos)

organism: Anas platyrhynchos


title: Illumina HiSeq 2500 (Burkholderia thailandensis)

organism: Burkholderia thailandensis


title: RN1100_Rat_MI_ReadyArray

city: Miami

first: Tongyu

last: Wikramanayake

state: FL

address: 1600 NW 10th Avenue, RMSB 2023A

department: Dermatology and Cutaneous Surgery

institute: University of Miami Miller School of Medicine

organism: Rattus norvegicus

distribution: commercial


title: Agilent-084552 Human Genome CGH Microarray

city: Houston

first: James

last: Lupski

state: Texas

address: One Baylor plaza

department: MHG

institute: BCM

organism: Homo sapiens


title: Nimblegen design ID 35739 Lysobacter enzymogenes OH11

city: Nanjing

first: Wang

last: Yansheng

address: No.1 Weigang

department: Department of Plant Pathology

institute: Nanjing Agricultural University

organism: Lysobacter enzymogenes

description:
NimbleGen design name 110809_Xory_YR_exp, NimbleGen design ID 35739.  5,180 probes were designed for detection of  5,180 genes from Lysobacter enzymogenes OH11. The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
native array description file: 110809_Xory_YR_exp.ndf
native array description file: 110809_Xory_YR_exp.ngd

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


title: zebrafish mTOR Signaling RT² Profiler™ PCR Array (Qiagen)

status: Public on Jun 23 2017

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

institute: Institute of Hydrobiology, Chinese Academy of Sciences

organism: Danio rerio

technology: RT-PCR

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

manufacture_protocol: see manufacturer's website


title: PROSTVAC a96 ver. 2

organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Sus scrofa domesticus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius


title: Agilent-018403 human DMD HD-CGH array [hg19]

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description:
dystrophin CGH

Arrays of this design have barcodes that begin with 16018403 or 2518403.

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: Zebrafish PI3K-AKT Signaling Pathway RT2 Profiler PCR Array (Qiagen)


title: Illumina HiSeq 2000 (Oncopeltus fasciatus)

organism: Oncopeltus fasciatus


title: Agilent-026822 026822_D_20100107 [Probe name version]

city: Thousand Oaks

first: Dan

last: Baker

state: CA

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

description:
Human gene expression custom Amgen array 4x180K.

Arrays of this design have barcodes that begin with 16026822 or 2526822.

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


title: Illumina NextSeq 500 (Streptococcus salivarius)

organism: Streptococcus salivarius


title: Lactobacillus_135k array

status: Public on Jun 22 2017

city: Aurillac

first: Stephanie

last: Bornes

address: 100 rue de l'egalite

department: IUT genie biologique

country: France

institute: Universite d'Auvergne

organism: Lactobacillus

description:
NimbleGen design name 110518_Lactobacillus_str_AN, NimbleGen design ID 552981.  A 1:2 expression design for 7,303 genes from 25 Lactobacillus species with 2 or 3 45-60-mer probe pairs (PM/MM) per gene.
Each probe is replicated 3 times.  The design includes random GC and other control probes.


title: Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S)


title: Illumina Genome Analyzer (Cymbidium tortisepalum var. longibracteatum)

status: Public on Jun 20 2017

organism: Cymbidium longibracteatum


title: Agilent-079141 PPCD1-3_loci G4126A 8X60 array (Feature number version)

status: Public on Jun 21 2017

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description:
Agilent-079141 PPCD1-3_loci  G4126A
Array design is based on genome build hg19/GRCh37.
Arrays of this design have barcodes that begin with 16079141 or 2579141
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: NimbleGen Human 100309_AS_human_100426_pz array [MATCH_INDEX version]

city: Beijing

first: Jin

last: Song

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

description:
DESIGN_ID: 11583
designname: 100309_AS_human_100426_pz


title: Illumina HiSeq 2000 (Meyerozyma caribbica)

organism: Meyerozyma caribbica


title: Illumina HiSeq 2500 (Yersinia pestis)

organism: Yersinia pestis


title: Illumina HiSeq 2500 (Ramichloridium luteum)

organism: Ramichloridium luteum


title: SABiosciences/Qiagen Human Mitochondrial Energy Metabolism (PAHS-008Z)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
Mitochondrial energy metabolism array PCR assay panel
Qiagen RT² Profiler panel of PCR arrays


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

status: Public on Jun 15 2017

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

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
June 03, 2009: annotation table updated with netaffx build 28
June 06, 2012: annotation table updated with netaffx build 32

first: Domenica

last: Ronchetti

first: Antonino

last: Neri

manufacture_protocol:
see manufacturer's web site
Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts
All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).


title: Illumina NextSeq 500 (Mus)

status: Public on Jun 30 2017

organism: Mus


title: MITOMI 2.0 JokerCake 8mer library (microfluidic affinity assay)

status: Public on Jun 19 2017

city: Stanford

first: Polly

middle: Morrell

last: Fordyce

address: 443 Via Ortega

department: Genetics, Bioengineering

institute: Stanford University

organism: synthetic construct

description:
de Bruijn Joker synthetic library
spotted oligonucleotide with aligned microfluidic device
MITOMI 2.0 experiment, 240 oligonucleotides, 4 replicates per oligonucleotide
The MITOMI 2.0 JokerCake 8mer library is a library of synthetically designed sequences designed to include all possible 8mer DNA sequences in a minimally compact space by including degenerate 'joker' characters (N = approx. equimolar mixture of A, C, G, and T). These designed library sequences are ordered as linear oligonucleotides from IDT and then converted to Alexa-647-labeled dsDNA via annealing of an Alexa-647-labeled universal probe to the 3' end of each oligonucleotide, followed by extension using Klenow Fragment, exonuclease -.

manufacture_protocol:
1. Oligos are ordered from IDT in shalllow 96 well plates.  Each well is concentration- and volume-normalized to contain 50 uL of 100 uM oligonucleotide.
2. Create a daughter plate at 25 uM by removing 5 uL of 100 uM oligonucleotide and adding 15 uL ddH20.
3. Convert DNA to fluorescently-labeled dsDNA via steps 4-7.
4. In each well of a new 96 well plate, combine 1.5 uL dNTPs at 10 mM each, 1.5 uL ddH20, 1.0 uL NEBuffer 2, 3.0 uL library primer at 25 uM, and 3.0 uL 25 uM Alexa-647-labeled primer.
5. Melt DNA at 95C for 3 minutes, slow anneal to 25C over 45 minutes.
6. To each well, add 0.2 uL Klenow exo-, 0.5 uL NEBuffer 2, and 4.3 uL ddH20.
7. Heat to 37C for 60 minutes for Klenow extension; deactivate Klenow by heating to 72C for 20 minutes.
8. Transfer fluorescently-labeled dsDNA to a 384 well plate and dilute to 1.25 uM DNA in a solution of 2% BSA and 12.5 mg/mL trehalose in 3x SSC.
9. Print fluorescently-labeled dsDNA onto ThermoFisher SuperChip epoxysilane-coated slides.
10. Follow standard MITOMI device protocols for surface treatments and measurements.


title: Illumina HiSeq 2500 (Setaria viridis)

last: GEO

organism: Setaria viridis


title: Illumina HiSeq 2500 (Vuilleminia comedens)

status: Public on Jun 16 2017

organism: Vuilleminia comedens


title: Ion Torrent Proton (Mus)


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

status: Public on Jun 14 2017

city: Nasushiobara

first: Ryo

last: Okada

state: Tochigi

address: 768 Senbonmatsu

department: Forage Crop Research Division

country: Japan

institute: NARO Institute of Livestock and Grassland Science

organism: Oryza sativa

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


title: Illumina MiSeq (Francisella tularensis subsp. holarctica LVS)


title: NimbleGen Arabidopsis thaliana expression array [2006-08-28_Arabidopsis_60mer_expr]

city: Beloit

first: Amy

middle: Graham

last: Briggs

state: WI

address: 700 College St.

department: Biology

institute: Beloit College

organism: Arabidopsis thaliana

description:
Expression design for Arabidopsis thaliana (TAIR6.0). 6 60mer probes per gene, 2 replicates. 30387 exemplar genes representing a total of 30510 transcripts/variants.
Arabidopsis thaliana Col-0 TAIR6.0

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


title: Illumina NextSeq 500 (Clostridium beijerinckii)

organism: Clostridium beijerinckii


title: BGISEQ-500 (Apostichopus japonicus)

organism: Apostichopus japonicus


title: Illumina HiSeq 2500 (Enterococcus faecium)

organism: Enterococcus faecium


title: Illumina HiSeq 2000 (Manis javanica)

organism: Manis javanica


title: Agilent Custom Chickpea Gene Expression  8X60K Array (AMADID: 037094) designed  by Genotypic Technology Private Limited

status: Public on Jun 13 2017

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Plant Genome Research

organism: Cicer arietinum


title: Custom pangenomic 4 X 72 K Nimblegen array (eight strains of  Propionibacterium freudenreichii)

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

organism: Propionibacterium freudenreichii

description:
Propionibacterium freudenreichii strains CIRM121, CIRM122, CIRM129, CIRM134, CIRM139, CIRM456, CIRM514, and CIRM516.
The design allows to monitor the expression of 2,740 genes (clusters) based on probing 27,546 distinct genomic regions (only 594 genes found in at least 1 of the 8 strains were not covered). On average, the expression of a gene was monitored via 10 distinct probe sequences (corresponding to 20 measures of intensity since each probe was duplicated).
120412_Pfreundenreichii_VL_exp.ndf
120412_Pfreundenreichii_VL_exp_X4.ncd

manufacture_protocol: 4 X 72K probes Nimblegen microarray. For the probe design we used the Oligowiz software (Wernersson and Nielsen, 2005) and a reference pangenome composed of a representative sequence for each gene cluster to build a repertoire of possible isothermal probes of length between 45 nt and 65 nt. A relatively high target melting temperature 90°C (+/- 5°C) was selected to account for the high G+C-content of Pf (67%). Then, we proceeded to the probe selection according to two criteria. First, we required at least 45 nt between the 5'-ends of two adjacent probes on the reference sequence (implying the overlap to be less than 20 nt). Second, we preferred probes corresponding to genomic regions without SNPs and discarded all probes whose sequences contained more than two mismatches between any of the 8 genomes and the reference pangenome. When SNPs existed, we included in the design a perfect match variant for each probe allele in the 8 genomes, and only perfect match variant was used to measure gene expression. For technical reasons, probes requiring more than 148 synthesis cycles were also filtered out. Finally, all probes were duplicated.


title: RiboBio Human lncRNA+mRNA Microarray (A10312-90-2)

status: Public on Jun 12 2017

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

institute: GEORGE WASHINGTON UNIV

organism: Homo sapiens

technology: spotted DNA/cDNA

description: Contains 41531 lncRNA probes and 33352 mRNA probes.


title: GeneSeek HD Bovine 77k Genotyping Array

city: Yangli

first: Chuzhao

last: Lei

state: Shannxi

address: Xinong Road

institute: Northwest Agriculture and Forestry University

organism: Bos taurus

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website


title: Illumina NextSeq 500 (Mycobacterium tuberculosis H37Rv)

organism: Mycobacterium tuberculosis H37Rv


title: Illumina NextSeq 500 (Armillaria ostoyae)

organism: Armillaria ostoyae


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [Mm_ENTREZG_v18]

organism: Mus musculus

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Rattus)

organism: Rattus


title: Human miRNA Array miRbase release 19

city: Luoyang

first: Jiachun

last: Sun

state: Henan

address: 24 Jinghua road, Jianxi district

institute: Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology

description:
Part No.: MRA-1001B1C
Human miRNA Array
Version No. miRHuman_19_HUST_121206

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: ISCI3 Custom human Delta Gene  BioMark 96.96 Dynamic Array

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

manufacture_protocol: see manufacturer's website. PCR assay


title: [hGlue_3_0] Custom Affymetrix Human Transcriptome Array

city: Boston

first: Rulla

middle: M

last: Tamimi

state: MA

address: 181 Longwood Avenue

department: Medicine

institute: Brigham and Women's Hospital

description:
hGlue3_0.r1.TC_Annov.txt: Original annotation file from Affymetrix.
FFPE_annotations_NCBIupdated_18427probes_18417genesymbol_7Dec15.txt: Annotation file which updates the Entrez Gene IDs and symbols; if multiple probesets mapped to a single gene, the most variable probe was selected to represent the gene.

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


title: NimbleGen T. erythraeum IMS101 expression plus tiling of intergenic regions 4x72K array [080610_Trich_erth_UCSC_TS_expr]

status: Public on Jun 11 2017

city: Xiamen

first: Tuo

last: Shi

state: Fujian

address: No. 1 South Xiang'an Rd.

institute: Xiamen University

organism: Trichodesmium erythraeum IMS101

description:
NimbleGen design name 080610_Trich_erth_UCSC_TS_expr, NimbleGen design ID 7738. A whole genome ORF-based expression design for 4788 genes from Trichodesmium erythraeum IMS101 with up to six 60-mer probes per gene, plus tiling of 60-mer probes at a 150-bp interval for intergenic regions >60bp in length. Each ORF-based probe is replicated 2 times. The design includes random GC and other control probes. The final microarray slides were printed in 4-plex (4x72K) format.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files.
GenBank accession number of Trichodesmium erythraeum IMS101 = NC_008312


title: Agilent-018818 human 8x60k oligo microarray [CCDP_AGILENT_V2_30BP; Probe Name version]

status: Public on Jun 10 2017

city: Yokohama-shi, Tsurumi-ku

last: Matoba

state: Kanagawa-ken

institute: DNAChipResearchInc

manufacture_protocol: Custom Oligo Microarray 8x60k (Design ID: 018818)see manufacturer's web site at http://www.agilent.com/


title: Illumina HiSeq 2000 (Obba rivulosa)

status: Public on Jun 09 2017

organism: Obba rivulosa


title: [CanGene-1_1-st] Canine Gene 1.1 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Canis lupus familiaris

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

June 09, 2017: annotation table updated with netaffx build 36


title: Illumina MiSeq (Sindbis virus)

organism: Sindbis virus


title: Custom human cDNA microarray (HUMLIB384)

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

institute: Bologna University

manufacturer: Unilever Discover, Colworth Science Park, Sharnbrook MK44 1LQ, UK

manufacture_protocol: 19800 total probes, comprising: 18,664 unique genes from CompuGen Human OligoLibrary V1.0 (cat# HUMLIB384); 748 custom probes and 388 internal controls. Each oligo has a 5' C6-amino linker enabling covalent attachment to the substrate. Oligonucleotides were resuspended in phosphate buffer and printed onto Codelink slides (GE Healthcare, Amersham, St.Giles, UK) using a Biorobotics TAS microarray system. Probe labeling was performed using the Genisphere 350HS labeling system (Hatfield, PA, USA) according to the manufacturer?s standard protocol.


title: Agilent-025821 Custom Salmonella Enteritidis Array

city: Rennes

first: Florence

last: Baron

address: 65 rue de Saint Brieuc

institute: Agrocampus Ouest

organism: Salmonella enterica subsp. enterica serovar Enteritidis

manufacture_protocol: Array Agilent technology, DesignID=025821


title: Agilent-048908 8x60K whole genome incl V1-V2 linc BioVacSafe final 048908 [Probe Name version]

city: Bethesda

first: GEO

last: admin

institute: NCBI/NLM/NIH

description:
Mattick linc
BROAD linc
Arrays of this design have barcodes that begin with 16048908 or 2548908.

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


title: Illumina NextSeq 500 (Lepidobatrachus laevis)

status: Public on Jun 08 2017

organism: Lepidobatrachus laevis


title: Illumina HiSeq 2000 (Lepidobatrachus laevis)


title: Illumina HiSeq 2000 (Lysinibacillus varians)

organism: Lysinibacillus varians


title: Illumina HiSeq 2000 (Mus)

organism: Mus


title: Agilent-016322 Whole Genome Saccharomyces cerevisiae 8x15K (Probe name version)

city: Mohali

first: Anand

middle: K

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli PO

department: Department of Biological Sciences

institute: Indian Institute of Science Education and Research, Mohali

organism: Saccharomyces cerevisiae

description: Agilent Whole Genome Saccharomyces cerevisiae 8x15K (AMADID: 016322).


title: Illumina HiSeq 2500 (Halobacterium salinarum NRC-1)

status: Public on Jun 06 2017

organism: Halobacterium salinarum NRC-1


title: Agilent-020026 VPC Human 105K v1

status: Public on Jun 07 2017

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description: *annotation from RefSeq and EntrezGene Database (downloaded: April, 2012)

manufacture_protocol: SurePrint 2x105K format, feature and microarray designed using eArray


title: Illumina HiSeq 2500 (Rhizophagus irregularis)

status: Public on Jun 05 2017

last: GEO

organism: Rhizophagus irregularis


title: Illumina HiSeq 2000 (Vitis labrusca)

organism: Vitis labrusca


title: Illumina HiScanSQ (Anopheles stephensi)

organism: Anopheles stephensi


title: Illumina HiSeq 2000 (Vitis acerifolia)

organism: Vitis acerifolia


title: Illumina HiSeq 2000 (Vitis cinerea)

organism: Vitis cinerea


title: SAGE:22:NlaIII:Coprinopsis cinerea

status: Public on Jun 02 2017

organism: Coprinopsis cinerea

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Coprinopsis cinerea using NlaIII as an anchor enzyme.


title: Illumina MiSeq (Human betaherpesvirus 5)

organism: Human betaherpesvirus 5


title: Illumina HiSeq 2500 (Human betaherpesvirus 5)


title: OpArray Human 35K (OpHuman_v4_0_3_2007July_geneID.GAL)

status: Public on Jun 03 2017

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

organism: Homo sapiens

manufacture_protocol: See manufacturer website


title: NanoString nCounter human miRNA expression system

status: Public on Jun 01 2017

first: Athalia

middle: Rachel

last: Pyzer

address: 3 Blackfan Circle CLS 724

institute: BIDMC

technology: other

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


title: [Agilent-064832] C. elegans gene expression 8x44K olig array

city: Vicksburg

first: Ping

last: Gong

state: Mississippi

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: U.S Army Engineer Research and Development Center

organism: Caenorhabditis elegans

description: An Agilent C. elegans-specific microarray was custom-designed using Agilent catalog probes. It contained 42862 probes targeting 28164 unique genes, among which 76.6% or 21562 genes had a single probe, 23.4% or 6596 genes had 2 to 12 probes, and the remaining 6 genes had 13, 15, 20, 26, 27 and 37 probes, respectively. These probes were assembled from three existing Agilent catalog probe groups: PGRID51529TDT (512 probes), PGRID51764TDT (50), and PGRID51763TDT (42300). These 60-mer oligo probes, together with 1319 control probes, were printed in situ on a 364-row by 164-column array grid in an 8-array-per-slide format, yielding a 70% occupancy of 62976 available spots.

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


title: Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray (miRNA_107_Sep09)

city: Seoul

first: Eun Ji

last: Nam

address: 50 Yonsei-ro

department: Obstetrics and Gynecology

institute: Yonsei University College of Medicine

description:
Feature Number version of this Array is GPL15018

Human and human viral miRNAs


title: Illumina NextSeq 500 (Komagataella phaffii)

organism: Komagataella phaffii


title: Illumina HiSeq 2000 (Drosophila melanogaster; Drosophila mojavensis; Drosophila persimilis)

organism:
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis


title: Ion Torrent Proton (Staphylococcus aureus subsp. aureus USA300_FPR3757)


title: Agilent-044025 USDA_FADDL_PV_180k_V5

status: Public on May 26 2017

city: Greenport

first: Michael

middle: T

last: McIntosh

state: NY

address: Plum Island Animal Disease Ctr, PO Box 848

department: NVSL

institute: USDA APHIS VS STAS

organism: Viruses

first: Roger

last: Barrette

manufacture_protocol: custom spotted, non-degenerate synthetic oligonucleotides, average size 60nt, in a 4x180k format


title: [OElncRNAs520855F] Affymetrix Human OElncRNAs520855F Array [probe set (exon) version]

city: Shenyang

first: Fengxue

last: Geng

state: Liaoning

address: Nanjing North St. 117, Heping District

department: Periodontics

institute: China Medical University

description:
#%create_date=Tue Jul 21 17:22:18 PDT 2015
#%chip_type=OElncRNAs520855F
#%lib_set_name=OElncRNAs520855F
#%lib_set_version=r1
#%genome-species=Homo sapiens
#%netaffx-annotation-data-type=probe_set
#%guid=a4a3cc34-f47d-4407-9cd6-1c10fa5726bc
#%annotation-version=design-time

first: Yaping

last: Pan

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


title: [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0 [CDF: Brainarray mta10_Mm_ENTREZG_v20]

state: MD

address: 9000 Rockville Pike

organism: Mus musculus

relation: Alternative to: GPL20775 (transcript (gene) CSV version)

relation: Alternative to: GPL20258 (transcript (gene) CDF version)

manufacture_protocol: See manufacturers website


title: [OElncRNAs520855F] Affymetrix Human OElncRNAs520855F Array [transcript (gene) version]

description:
#%create_date=Mon Jul 06 12:49:08 PDT 2015
#%chip_type=OElncRNAs520855F
#%lib_set_name=OElncRNAs520855F
#%lib_set_version=r1
#%genome-species=Homo sapiens
#%genome-version=hg38
#%netaffx-annotation-data-type=transcript_cluster
#%guid=56f2cd96-2c5c-44ae-a9b0-55bba6d36f82


title: Illumina HiSeq 2000 (Drosophila ananassae; Drosophila willistoni; Drosophila yakuba)

organism:
Drosophila ananassae
Drosophila yakuba
Drosophila willistoni


title: BC013_nirS

status: Public on May 02 2017

city: Gulf Breeze

first: Jessica

middle: Anne

last: Lisa

state: FL

address: 1 Sabine Island Drive

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

organism: uncultured bacterium

description: The probes on this array are 90-mers that consist of the 70-mer nirS sequence and a 20-mer universal reference sequence.

manufacture_protocol:
1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50%  DMSO and were spotted on CMT-GAPS amino silane-coated  glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: Agilent-066813 Nicotiana benthamiana N.bentham_transcriptome_v3

status: Public on Jan 08 2016

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

organism: Nicotiana benthamiana

description:
Nicotiana benthamiana transcriptome v.3 (Nakasugi et al. 2013 PlosOne) and partially transcriptome v.5 (Nakasugi et al. 2014 PlosOne). Sense orientation of target transcripts has been verified with hybridization and similarity searches (Goralski et al. 2016)
Arrays of this design have barcodes that begin with 16066813 or 2566813.
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 (Ciona robusta)

organism: Ciona robusta


title: Illumina HiSeq 2000 (Staphylococcus aureus)

status: Public on Jul 15 2013

organism: Staphylococcus aureus


title: [Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) Genome Array

status: Public on Jul 01 2004

state: CA

organism: Vitis vinifera

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® Vitis vinifera Genome Array is the first array to provide comprehensive coverage of the V. vinifera genome.

14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species can be interrogated.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Sixteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip® Vitis vinifera (Grape) Genome Array. Sequences used in the design of the V. vinifera Genome Array were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 7, Oct 2003).

Annotations derived from Affymetrix CSV file dated 6/23/2004

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Staphylococcus aureus)

status: Public on Jul 28 2014


title: Illumina HiSeq 2000 (Escherichia coli)

status: Public on Sep 08 2011

organism: Escherichia coli


title: Agilent-048908 8x60K whole genome incl V1-V2 linc BioVacSafe final 048908 [Feature Number version]

status: Public on Dec 23 2015

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description:
Mattick linc
BROAD linc
Arrays of this design have barcodes that begin with 16048908 or 2548908.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina MiSeq (Danio rerio)

status: Public on May 20 2016

organism: Danio rerio


title: Illumina HiSeq 3000 (Arabidopsis thaliana)

status: Public on Nov 27 2015

organism: Arabidopsis thaliana


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array

status: Public on Jul 18 2002

last: Affymetrix

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

June 03, 2009: annotation table updated with netaffx build 28
June 07, 2012: annotation table updated with netaffx build 32
July 01, 2016: annotation table updated with netaffx build 35

relation: Alternative to: GPL8455 (Alternative CDF)

relation: Alternative to: GPL10050 (Alternative CDF)

relation: Alternative to: GPL10948 (Alternative CDF)

relation: Alternative to: GPL10868 (Alternative CDF)

relation: Alternative to: GPL13230 (Alternative CDF [ATH1-121501.TAIR9])

relation: Alternative to: GPL13838 (Alternative CDF [Brainarray TAIRG, V.12.1.0])

relation: Affiliated with: GPL16112 (Alternative CDF [ATH1121501_At_TAIRG, v14.0.0])

relation: Affiliated with: GPL18395 (Alternative CDF [Lepidium_LsRNA_FDRp01_ANOVA_Probes_Keep_3probe])

relation: Alternative to: GPL21063 (Alternative CDF [ATH1121501_At_TAIRG, v18.0.0])

manufacture_protocol:
see manufacturer's web site

The current release has 22810 entries and was indexed 26-Jun-2003.
Annotation data from TAIR, Gene Ontology Consortium and TIGR were mapped to the Arabidopsis ATH1 Array probe sets. The AGI (Arabidopsis Genome Initiative) ID (e.g. AT5G23000) corresponding to the gene represented on the array was used to map annotation data obtained from TAIR, Gene Ontology and TIGR databases. Similarly, gene title and gene symbol, as well as the EC annotations for the AGI ID were extracted from the TIGR database.  These annotation mappings were validated by a two-pronged approach. First, probe sets were randomly selected and manually curated to check for consistency between Gene Ontology terms, gene title and protein domain associations. Furthermore, associations within and between data sets from different public databases were also used to check for consistencies. For example, consider the association of gene ontology terms and InterPro IDs. Several Gene Onoltogy terms have InterPro ID(s) curated as supporting evidence for assigning the term to an AGI locus. This relationship was used to validate the consistency of the ontology terms from Gene Onotlogy and InterPro domain annotations from TAIR.  The GeneChip® Arabidopsis ATH1 Genome Array contains more than 22,500 probe sets representing approximately 24,000 genes. Sequences used in the design were selected and clustered in collaboration with TIGR and were derived from TIGR's ATH1-121501 Database. Oligoneuclotide probes are synthesized in situ to each corresponding sequence. Eleven pairs of oligoneuclotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Arabidopsis ATH1 Genome Array. Most sequences represented on the previous generation GeneChip® Arabidopsis Genome Array are also represented on the ATH1 array. Due to the dynamic nature of public databases, probe sets for these sequences will not be identical and in some cases will be represented by a completely new probe set. As a result, data generated with different versions of the Arabidopsis array may not always produce concordant results. The probe arrays are for research use only and not intended for use in diagnosis of diseases.


title: Illumina HiSeq 2000 (Zea mays)

status: Public on Apr 18 2012

organism: Zea mays


title: Illumina HiSeq 4000 (Sus scrofa)

status: Public on Sep 23 2016

organism: Sus scrofa


title: [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0 [transcript (gene) CSV version]

status: Public on Aug 05 2015

description:
Annotation was derived from the Affymetrix annotation file MTA-1_0.na35.mm10.transcript.csv:

#%create_date=Wed Apr  1 16:56:09 2015 PDT
#%chip_type=MTA-1_0
#%lib_set_name=MTA-1_0
#%lib_set_version=r1
#%genome-species=Mus musculus
#%genome-version=mm10
#%genome-version-ucsc=mm10
#%genome-version-ncbi=38
#%genome-version-create_date=2011-12-00
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-species=Mus musculus
#%genome-lifted_from-version-ucsc=mm10
#%genome-lifted_from-version-ncbi=38
#%netaffx-annotation-date=2014-10-31
#%netaffx-annotation-netaffx-build=35

relation: Alternative to: GPL20258 (Affymetrix Transcript CDF Version)

relation: Alternative to: GPL23535 (Alternative CDF [Brainarray mta10_Mm_ENTREZG_v20])


title: Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Feature Number version)

status: Public on Apr 15 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Homo sapiens

description:
Human 44k Content Refresh

Arrays of this design have barcodes that begin with 16026652 or 2526652.

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 GPL13497


title: Illumina HiSeq 2500 (Gallus gallus)

organism: Gallus gallus


title: Illumina HiSeq 4000 (Danio rerio)

status: Public on Apr 15 2016


title: Illumina Genome Analyzer IIx (Mus musculus)

status: Public on Sep 30 2010