title: Illumina NextSeq 500 (Streptococcus mutans DSM 20523)

status: Public on Mar 30 2022

last: GEO

country: USA

organism: Streptococcus mutans DSM 20523

technology: high-throughput sequencing

distribution: virtual


title: nCounter human 289-immuno-gene panel

status: Public on Jun 19 2022

city: Nanjing

first: Xiangyi

last: Kong

address: Hanzhong road

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

organism: Homo sapiens

technology: other

distribution: custom-commercial


title: Resolve Biosciences Molecular Cartography custom platform

status: Public on Sep 01 2022

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

organism: Mus musculus

description:
The Platform's ~100 genes are the customized genes. The platform can work with other customized genes as well.
The platform applies molecular cartography probes.
Probe sequences are proprietary.

manufacture_protocol: Protocol provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063


title: Nanostring nCounter PanCancer IO 360 Panel

status: Public on May 05 2022

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

manufacture_protocol: See manufacturer's website.


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [mogene20st_Mm_ENTREZG_24.0.0]

status: Public on Mar 23 2022

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

technology: in situ oligonucleotide

manufacture_protocol: This Platform is identical to GPL16570 but a custom CDF environment was used to extract data [Brainarray Version 24, mogene20st_Mm_ENTREZG].


title: Delta gene expression assay with Fluidigm 96 dynamic array

status: Public on Mar 19 2022

city: Paris

first: Olivia

last: Bonduelle

address: 91 bd de l'Hopital

country: France

institute: INSERM U1135

technology: RT-PCR

description:
Fluidigm 96 dynamic array. PCR assay
As a result of the lognormal distribution described by Bengtsson et al. (2005) and others, it is useful to view single-cell data as expression level above detection limit on a log scale. For qPCR data, it is convenient and appropriate to do this in Log2 by defining the term Log2Ex: Log2Ex = LoD Ct ? Ct [Gene]. ?If the value is negative, Log2Ex = 0. ?For more information on this value, see K.J. Livak et al., Methods (2012),http://dx.doi.org/10.1016/j.ymeth.2012.10.004.

manufacture_protocol: see manufacturer website: Real-Time PCR Analysis protocol user guide and "Two-step single-cell gene expression using EvaGreen Supermix on the BioMark and BioMark HD systems, protocol C"


title: NanoString Human nCounter PanCancer IO360 Panel

status: Public on Apr 02 2022

city: St Louis

first: Jose

middle: P

last: Zevallos

state: MO

address: 660 South Euclid Avenue, Campus Box 8115

department: Otolaryngology - Head and Neck Surgery

institute: Washington University School of Medicine

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


status: Public on Mar 18 2022

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This Platform is identical to GPL16570 but a custom CDF environment was used to extract data [Brainarray Version 24, mogene20st_Mm_ENTREZG].

manufacture_protocol: See manufacturer's web site.


title: Human Oligo chip 25k

city: Tokyo

first: Kyaw Min

last: Soe

state: Tokyo

department: Orthognathics

country: Japan

institute: TMDU

technology: spotted DNA/cDNA


title: Composite array platform for Corynebacterium glutamicum ATCC 13032

status: Public on Jul 22 2022

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism: Corynebacterium glutamicum ATCC 13032

description:
This platform represents Corynebacterium glutamicum transcript information for studies performed with a wide variety of array platforms.
This platform is based on genome accession: BX927147

distribution: non-commercial

manufacture_protocol: manufacture protocol


title: Nanostring codeset Mouse Immune Exhaustion Panel [NS_Mm_Exhaustion_v1.0]

status: Public on Mar 14 2022

city: Atlanta

first: Rae

last: Hunter

state: Georgia

address: 1760 Haygood Drive NE

department: Pediatrics

institute: Emory University

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


title: Agilent Custom Mycobacterium smegmatis Whole Genome 8x15k GE Microarray (AMADID-43029)

status: Public on Mar 10 2022

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: Mycolicibacterium smegmatis

description: Agilent Genotypic Technology designed Custom Mycobacterium smegmatis Whole Genome 8x15k GE Microarray (AMADID-43029)


title: [Clariom_S_Human] Affymetrix Clariom S Assay

status: Public on Mar 31 2022

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne


title: Axion Tea SNP

status: Public on Mar 09 2022

city: Hangzhou

first: Liu-Bin

last: Wang

address: 9 South Meiling road

department: Tea Research Institute

institute: Chinese Academy of Agricultural Sciences

organism: Camellia sinensis

manufacture_protocol: see manufacturer's web site


title: [Clariom_S_Human] Affymetrix Clariom S Human array [ClariomSHuman_Hs_ENSG_25.0.0]

status: Public on Mar 15 2022

city: Salamanca

first: Rogelio

last: González-Sarmiento

state: Salamanca

address: Alfonso X el Sabio, sn

department: Medicine

country: Spain

institute: University of Salamanca


title: Agilent-068043 Whole Genome Escherichia coli 8x15K designed by Genotypic Technology Private Limited [Probe Name version]

status: Public on Mar 05 2022

organism: Escherichia coli


title: Agilent-070156 Human_miRNA [Feature Number version]

status: Public on Mar 08 2022

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

institute: Hirosaki university

distribution: commercial

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


title: Custom Nanostring nCounter human PanCancer Immune Profiling panel

status: Public on Mar 01 2022

city: Aarhus

first: Ulvi

last: Ahmadov

state: Denmark

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

description: nCounter PanCancer Immune Profiling Panel (cat# XT-CSO-HIP1-12) plus a custom made PanelPlus of the following genes: NFE2L2, TMEM173, MB21D1, IFNLR1, irf9, IFNL3, IFNL4, AIM2, TREX1, ENPP1, PCBP1, PQBP1, G3BP1, STIM1, LRRC8A, SLC19A1, NLRC3, NLRX1, ZDHHC1, TRIM56, TRIM32, RNF5, ULK1, TTLL4, TTLL6, AGBL5, AGBL4, PRKDC, DDX41

manufacturer: NanoString Technologies, Inc.; Seattle, WA


title: Geochip 5.0

city: Yangling

first: jingjing

last: li

address: xi nong road 26

institute: Northwest A&F University

organism:
Bacteria
Archaea
Eukaryota
Viruses

manufacture_protocol: custom


title: Agilent-069048 Bifidobacterium bifidum 0140801_Bbi

status: Public on Dec 31 2021

city: Kunitachi

first: Eiji

last: Ishikawa

address: Izumi 5-11

institute: Yakult Central Institute

organism: Bifidobacterium bifidum

description:
Arrays of this design have barcodes that begin with 16069048 or 2569048.

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 GPL30211

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


title: CIT-CGH Homo sapiens BAC 5.3K [HG19]

status: Public on Jul 05 2021

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

manufacture_protocol:
The IntegraChipTM microarray was designed by the CIT-CGH consortium (Olivier Delattre Laboratory, Curie Institute, Paris; Charles Theillet Laboratory, CRLC Val d'Aurelle, Montpellier; Stanislas du Manoir Laboratory, IGBMC, Strasbourg) and the company IntegraGenTM (http://www.integragen.com).
Bacterial artificial chromosome (BAC) clones were chosen to obtain a systematic coverage of the genome, and detailed coverage of regions containing genes previously implicated in carcinogenesis. The median gap between two successive clones is 600 kb. Four replicate spots were deposited on the slides. For each sample, 500-600 ng of sonicated DNA was labelled by Random-Priming (Bioprime Labelling kit, Invitrogen, Carlsberg, CA, USA) according to the suppliers\x{2019} instructions, but for 18h. For tumour DNA, final concentrations of nucleotides were 0.02 mM of dCTP-Cy5 (Amersham Biosciences), 0.1 mM of dATP, dGTP, dTTP and 0.025 mM dCTP. For control DNA, 0.04 dCTP-Cy3 (Amersham Biosciences), 0.2 mM of dATP, dGTP, dTTP and 0.05 mM dCTP. Labelled DNAs were purified using MicroSpin-G50 columns (Amersham Biosciences). COT Human DNA (70 \x{03bc}g, Roche Diagnostics) and Salmon Testes DNA (30 \x{03bc}g, Sigma Chemical Co.) were added to the mixed tumour and reference DNAs. They were subsequently concentrated using a microcon YM-30 (Millipore) and resuspended to obtain 200 \x{03bc}l of hybridization solution (final concentration: 50% formamide, 0.8 x SCC, 10% W/V dextran sulfate, 2% SDS, pH=7). Finally, the probes were pre-annealed for 3 hours at 37°C. Every step was carried out in the HS 4800 hybridization station (Tecan). Slide pre-treatment included rinsing with 2 x SSC, 0.1% SDS at 30 °C for 30s, 2 x SSC at 30 °C for 30s and drying. After probe injection, hybridization was performed for 68h at 37°C under low agitation. Four post-hybridization washes were carried out: 50% formamide, 2 x SSC, 0.1% SDS at 45 °C for 37 s, 4 times; 2 x SSC, 0.1% SDS at 45 °C for 37 sec, 4 times; 4 x SSC, 0.1 Tween 20 at 45 °C for 37 sec, 4 times; slides were finally nitrogen dried and scanned using a ScanArray 4000 (Packard Bioscience). Images were quantified using UCSF Spot 2.1cc (Jain et al., 2002).


title: Agilent-045666 JFS

status: Public on Mar 06 2022

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

organism: Trypanosoma cruzi

description:
Tcruzi clone Cl Brener array

Arrays of this design have barcodes that begin with 16045666 or 2545666.

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: NanoString nCounter Bovine BRD Arrival 60 Panel v1.0

status: Public on Mar 02 2022

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

organism: Bos taurus

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


title: [Clariom_D_Human] Affymetrix Human Clariom D Assay [transcript (gene) version] [CDF: ClariomDHuman_Hs_ENTREZG, v22]

city: Toronto

first: Mingyao

last: Liu

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

country: Canada

institute: University Health Network

manufacture_protocol: This is similar to GPL23126 but a custom CDF environment was used to extract data [Brainarray Version 22, ClariomDHuman]. CDF and other files can be downloaded from Brainarray (see web link below).


title: NIEHS Rat Chip v2.2

status: Public on Dec 01 2004

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

organism: Rattus norvegicus

description: This array was developed in-house at NIEHS, and used for gene expression profiling experiments. A complete listing of the genes on this chip is available at the following Web site: https://tools.niehs.nih.gov/maps/index.cfm


title: NIEHS Rat Chip v2.1

description:
This array was developed in-house at NIEHS, and used for gene expression profiling experiments. A complete listing of the genes on this chip is available at the following Web site: https://tools.niehs.nih.gov/maps/index.cfm
cDNA microarray chips were prepared according to DeRisi et al., 1996, Nat. Genet. 14, 457-460. The spotted cDNAs were derived from a collection of sequence-verified clones that covered the 3` end of the gene and ranged in size from 500 to 2000 base pairs (Research Genetics). M13 primers were used to amplify insert cDNAs from purified plasmid DNA in a 100 5l polymerase chain reaction (PCR) mixture. A sample of the PCR products (10 microliters) was separated on 2% agarose gels to ensure quality of the amplifications. The remaining PCR products were purified by ethanol precipitation, resuspended in ArrayIt buffer (Telechem, San Jose CA) and spotted onto poly-L-lysine-coated glass slides using a modified, robotic DNA arrayer (Beecher Instruments, Bethesda MD).
-- taken largely verbatim from Hamadeh et al., Toxicological Sciences 67, 219-231 (2002)


title: nCounter Human Tumor Signaling 360 Panel

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

country: South Korea

institute: KIRAMS

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


title: nCounter Human Tumor Signaling 360 Panel (illeum)

status: Public on Mar 13 2022


title: NIEHS Yeast Chip v1.0

status: Public on Oct 01 2004

organism: Saccharomyces cerevisiae

description:
This cDNA Yeast Chip was developed in-house at NIEHS.  A complete listing of the 6,218 open reading frames on this chip is available at the following website: https://tools.niehs.nih.gov/maps/index.cfm
cDNA microarray chips were prepared as previously described (DeRisi, Penland et al. 1996; Hauser, Vingron et al. 1998). The spotted cDNAs were derived from a collection of primers of yeast ORFs (Research Genetics, Carlsbad, CA).  These primers were used to amplify yeast cDNAs from genomic DNA in a 100µl PCR reaction mixture.  A sample of the PCR products (10 ul) was separated on 2% agarose gels to ensure quality of the amplifications.  The remaining PCR products were purified by ethanol precipitation, resuspended in ArrayIt Spotting Solution buffer (Telechem, San Jose CA) and spotted onto poly-L-lysine coated glass slides using a modified, robotic DNA arrayer (Beecher Instruments, Bethesda MD).


title: miRCURY LNA Universal RT microRNA PCR, 4x Human panel I+II in 384 well PCR plates (type R)

first: Luis

middle: Miguel

last: Rincon

address: Paseo de San Vicente 58-182

department: Cardiology

institute: Hospital Universitario de Salamanca

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Intestinal Microecology Detection Microarray Version 4.0

city: Changsha City of Hunan Province

first: xuan

last: peng

state: Hunan

address: 88 Xiangya Road

institute: Kaifu District, Changsha City, Hunan Province

organism: human gut metagenome

technology: spotted oligonucleotide

manufacture_protocol:
1.The Oligo probe was dissolved in a 96-well plate with 0.5×TE pH8.0 to a concentration of 200um.
2.Transfer 7.5ul of each probe to a new 96-well plate, incubate at 37°C with 1000units of T4 PNK phosphorylase in 1×T4 PNK phosphorylation buffer solution for 2 hours, and the total volume is 15ul.
3. Transfer the phosphorylated probe to 30°C, add 4.5ul of 500μM linker sequence, use 1000units of T4 DNA ligase and incubate for 20 hours in 1×T4 DNA ligation buffer, the total volume is 35ul.
4. After the probe is ligated, precipitate with isopropanol and dissolve in 50ul of 0.1M NaOH solution.
5. Modified with 8mM alkylating agent for 2 hours at 65°C, then precipitated and dissolved in 0.1M NaOH (containing 0.5M NaCl) at a concentration of 350-400ng/ul.
6. Transfer the probes to a Genetix 394-well plate and place them in the sample wells of the Qarray2 chip spotter.
7. Start the Qarray2 spotting machine to automatically spot samples. After completion, the chip is subjected to constant temperature and humidity treatment to help the probe be better fixed, and then the residual salt on the surface is washed off for use. The remaining probes were sealed with aluminum foil and stored frozen at -20°C.


title: NanoString nCounter Custom Panel for 19 genes (TCD026_C3530)

city: Bengaluru

first: Nagesh

last: Mandadi

address: Bellary Road, H.A. Farm Post, Hebbal, Bengaluru, Karnataka

department: Division of Genomics Resource

institute: ICAR-National Bureau of Agricultural Insect Resources

organism:
Xenorhabdus
Bombyx mori
Spodoptera frugiperda
Galleria mellonella
Drosophila melanogaster
Photorhabdus
Heterorhabditis bacteriophora


title: Illumina Genome Analyzer IIx (Staphylococcus aureus)

status: Public on Sep 13 2012

last: GEO

organism: Staphylococcus aureus


title: [Celegans] Affymetrix C. elegans Genome Array

status: Public on Jul 18 2002

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Caenorhabditis elegans

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

Has 22625 entries and was indexed 30-Apr-2002.
Sequence information used for the design of the C. elegans array was downloaded from the Sanger Center database on December 05, 2000 and from GenBank release 121. All sequences were functionally reannotated by Affymetrix for improved descriptions. Annotation data from Wormbase, Gene Ontology Consortium and Interpro were mapped to the C. elegans Genome Array probe sets.

Annotations derived from Affymetrix CSV file dated 5/19/2004

Keywords = high density oligonucleotide array
July 06, 2016: annotation table updated with netaffx build 35

relation: Alternative to: GPL13993 (Alternative CDF [Celegans_Ce_REFSEQ version 14.0.0])

relation: Alternative to: GPL13995 (Alternative CDF [Celegans_Ce_REFSEQ version 13.0.0])

relation: Alternative to: GPL18687 (Celegans_Ce_ENTREZG, Brainarray v16)

relation: Alternative to: GPL19846 (ENTREZG version 19)

relation: Alternative to: GPL32098 (Alternative CDF [Celegans_Ce_ENSG version 21])


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [transcript (gene) version]

status: Public on Jan 30 2013

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

Jan 30, 2013: annotation table updated with netaffx build 33

relation: Alternative to: GPL17408 (mogene20st_Mm_ENSG_17)

relation: Alternative to: GPL17791 (Alternative CDF)

relation: Alternative to: GPL18802 (Alternative CDF [mogene20st_Mm_ENTREZG_18.0.0])

relation: Alternative to: GPL20710 (Alternative CDF)

relation: Alternative to: GPL22598 (Alternative CDF [mogene20st_Mm_ENTREZG_20.0.0])

relation: Alternative to: GPL23092 (Alternative CDF [mogene20st_Mm_ENTREZG_21.0.0])

relation: Alternative to: GPL32068 (Alternative CDF [mogene20st_Mm_ENTREZG_24.0.0])

manufacture_protocol: See manufacturer's web site