title: NanoString nCounter GX NRF2 target gene expression

status: Public on Apr 30 2019

city: Pittsburgh

first: Chibueze

middle: Anthony

last: Ihunnah

state: Pennsylvania

address: Lothrop St, Pittsburgh, PA 15213

department: Medicine

country: USA

institute: University of Pittsburgh

organism: Homo sapiens

technology: other

distribution: custom-commercial


title: Illumina HiSeq 2500 (Bipolaris sorokiniana; Hordeum vulgare; Serendipita vermifera)

last: GEO

organism:
Hordeum vulgare
Bipolaris sorokiniana
Serendipita vermifera

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 3000 (Bipolaris sorokiniana)

organism: Bipolaris sorokiniana


title: Illumina HiSeq 2500 (Bipolaris sorokiniana; Hordeum vulgare)

organism:
Hordeum vulgare
Bipolaris sorokiniana


title: Illumina HiSeq 2500 (Hordeum vulgare; Serendipita vermifera)

organism:
Hordeum vulgare
Serendipita vermifera


title: Illumina NextSeq 500 (Prunus avium)

status: Public on Apr 29 2019

organism: Prunus avium


title: JC AMADID 084120

status: Public on Dec 19 2019

city: Boston

first: James

last: Anderson

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

organism: synthetic construct

technology: in situ oligonucleotide

manufacture_protocol: In situ oligosynthesized array with synthetic sequences containing the following classes of probes: (1) probes representing the predicted target site of all TALE proteins in this study as well as all mono- and di-nucleotide adjacent substitutions of these target sequences in constant flanking sequence, and (2) probes representing the predicted target sequences for an entirely different set of TALE proteins which are not relevant for this study and were not included in any of the experiments discussed here. AMADID 084120.


title: Illumina HiSeq 2500 (Deinococcus metallilatus)

status: Public on Apr 26 2019

organism: Deinococcus metallilatus


title: Operon Arabidopsis Version 3.0 microarray

status: Public on May 14 2019

city: Seoul

first: JiHye

last: Hwang

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha Womans University

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

manufacturer: The David Galbraith lab, University of Arizona

manufacture_protocol: 26,173 probes spotted with synthetic 70-mer oligonucleotides on aminosilane-coated slides


title: Agilent-017184 Mycobacterium smegmatis  4x44K

status: Public on Apr 25 2019

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

organism: Mycolicibacterium smegmatis

manufacture_protocol: Agilent


title: Illumina HiSeq 2500 (Macadamia integrifolia)

organism: Macadamia integrifolia


title: Illumina NovaSeq 6000 (Cucumis sativus)

organism: Cucumis sativus


title: Illumina HiSeq 2500 (Aspergillus oryzae RIB40)

status: Public on Apr 24 2019

organism: Aspergillus oryzae RIB40


title: Illumina HiSeq 3000 (Serendipita vermifera)

organism: Serendipita vermifera


title: Agilent-063206 Lachancea kluyveri array

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

organism: Lachancea kluyveri

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


title: Illumina HiSeq 3000 (Streptococcus pneumoniae TIGR4)

organism: Streptococcus pneumoniae TIGR4


title: Illumina HiSeq 3000 (Bipolaris sorokiniana; Serendipita vermifera)

organism:
Bipolaris sorokiniana
Serendipita vermifera


title: Illumina NextSeq 500 (Hordeum vulgare; Puccinia graminis f. sp. tritici)

organism:
Hordeum vulgare
Puccinia graminis f. sp. tritici


title: Illumina HiSeq 2500 (Mangifera indica)

organism: Mangifera indica


title: Illumina HiSeq 2500 (Linum usitatissimum)

organism: Linum usitatissimum


title: Illumina HiSeq 2500 (Persea americana)

organism: Persea americana


title: Illumina HiSeq 4000 (Anser cygnoides domesticus)

organism: Anser cygnoides


title: Illumina HiSeq 2000 (Bradyrhizobium diazoefficiens)

organism: Bradyrhizobium diazoefficiens


title: Illumina HiSeq 2500 (Hyphopichia burtonii)

status: Public on Apr 22 2019

organism: Hyphopichia burtonii


title: Ion Torrent PGM (Nitrospirillum amazonense)

organism: Nitrospirillum amazonense


title: Illumina HiSeq 3000 (Nezara viridula)

status: Public on Apr 19 2019

organism: Nezara viridula


title: Illumina HiSeq 2500 (Amphimedon queenslandica)

organism: Amphimedon queenslandica


title: Agilent-035148 SysteMTb V3

organism:
Mycobacterium tuberculosis variant bovis
Mycobacterium tuberculosis H37Rv

description:
Arrays of this design have barcodes that begin with 16035148 or 2535148.

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 NextSeq 500 (Vitis)

status: Public on Apr 18 2019

organism: Vitis


title: Illumina HiSeq 4000 (Schisandra chinensis; Vitis vinifera)

status: Public on Apr 23 2019

organism:
Vitis vinifera
Schisandra chinensis


title: Illumina HiSeq 2500 (Fundulus grandis)

status: Public on Apr 17 2019

organism: Fundulus grandis


title: Illumina HiSeq 2500 (Hyphopichia pseudoburtonii)

organism: Hyphopichia pseudoburtonii


title: NanoString nCounter Mouse Gene Expression Custom Chip MG534

city: Munich

first: Anja

last: Capell

state: Bavaria

address: Feodor-Lynen Str 17

department: Biomedical Center (BMC)

institute: Ludwig-Maximilians-University

organism: Mus musculus

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


title: Illumina HiSeq 4000 (Triticum polonicum)

organism: Triticum polonicum


title: Illumina HiSeq 4000 (Citrullus lanatus)

organism: Citrullus lanatus


title: Illumina HiSeq 2500 (Schisandra chinensis; Vitis vinifera)


title: Illumina NovaSeq 6000 (Sparassis latifolia)

organism: Sparassis latifolia


title: Illumina HiSeq 4000 (Callithrix jacchus)

organism: Callithrix jacchus


title: PacBio RS II (Streptococcus pyogenes)

organism: Streptococcus pyogenes


title: Agilent-084825 Bos taurus_ensembl_201704 Microarray (Probe Name Version)

city: Hachioji

first: Chiho

last: Yoshida

address: Takakura 9-1

country: Japan

institute: Agilent Technologies

organism: Bos taurus

description:
Bos taurus GE Array

Arrays of this design have barcodes that begin with 16084825 or 2584825.

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.
Target Sequence Source:  ensembl88 cdna and ncRNA transcripts
Gene expression array
Product Name :G4858A#84825 (Agilent)


title: Illumina HiSeq 2500 (Pseudomonas aeruginosa PAO1; Pseudomonas virus PA5oct)

organism:
Pseudomonas aeruginosa PAO1
Pseudomonas virus PA5oct


title: Illumina HiSeq 4000 (Pseudomonas putida)

organism: Pseudomonas putida


title: BGISEQ-500 (Drosophila melanogaster)

organism: Drosophila melanogaster


title: Illumina HiSeq 1000 (Lotus japonicus)

status: Public on Apr 14 2019

organism: Lotus japonicus


title: Illumina NovaSeq 6000 (Haemophilus influenzae R2866)

organism: Haemophilus influenzae R2866


title: MinION (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Illumina HiSeq 2500 (Ogataea parapolymorpha DL-1)

organism: Ogataea parapolymorpha DL-1


title: Illumina Hiseq 2500 (Gallus gallus)

status: Public on Apr 12 2019

organism: Gallus gallus


title: Illumina NovaSeq 6000 (Neurospora crassa)

organism: Neurospora crassa


title: Illumina Hiseq 2500 (Mus musculus)


title: Qiagen Human miRNome miScript miRNA PCR Array (MIHS-3216Z)

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

organism: Homo sapiens

technology: RT-PCR

description:
PCR assay
The Human miRNome miScript miRNA PCR Array (V16.0, 384-well) profiles the expression of the 1066 most abundantly expressed and best characterized miRNA sequences in the human miRNA genome (miRNome) as annotated in miRBase Release 16 (www.miRBase.org). Although they are well characterized, each of these miRNA sequences can regulate one to several messenger RNA transcripts, and conversely one mRNA can be regulated by one to several miRNA sequences. Therefore, the complex role that any given known miRNA sequence plays has yet to be completely defined. Use of the Human miRNome miScript miRNA PCR Array maximizes the likelihood of discovering miRNA sequences whose expression patterns correlate with the biological phenotypes under study. A set of controls included on each plate enables data analysis using the ΔΔCT method of relative quantification, assessment of reverse transcription performance, and assessment of PCR performance. The Human miRNome miScript miRNA PCR Array enables easy and reliable, SYBR Green-based real-time PCR analysis of the expression of 1066 miRNA sequences and discovery of those most important to the research area of interest.

distribution: commercial

manufacture_protocol: See manufacturer's website


title: Infinium Human Exome-12 v1.2 BeadChip

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: oligonucleotide beads

description: Descriptor File Name: HumanExome-12v1-2_B.bpm

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2500 (Triticum turgidum)

status: Public on Apr 11 2019

organism: Triticum turgidum


title: Illumina NextSeq 500 (Homo sapiens; Toxoplasma gondii RH)

status: Public on Apr 16 2019

organism:
Homo sapiens
Toxoplasma gondii RH


title: Illumina NovaSeq 6000 (Escherichia coli str. K-12 substr. MG1655)


title: Illumina HiSeq 2500 (Streptococcus oralis)

organism: Streptococcus oralis


title: NextSeq 550 (Glycine max)

organism: Glycine max


title: Illumina HiSeq 4000 (Bacteroides thetaiotaomicron VPI-5482)

status: Public on Apr 10 2019

organism: Bacteroides thetaiotaomicron VPI-5482


title: HiSeq X Ten (Papaver somniferum)

organism: Papaver somniferum


title: Illumina NextSeq 500 (Parascaris sp.)

status: Public on Apr 09 2019

organism: Parascaris sp.


title: Illumina NextSeq 500 (Labrus bergylta)

status: Public on Apr 08 2019

organism: Labrus bergylta


title: Illumina HiSeq 2500 (Aegilops tauschii)

organism: Aegilops tauschii


title: Illumina HiSeq 2500 (Citrus sinensis x Citrus trifoliata; Phytophthora parasitica)

organism:
Phytophthora nicotianae
Citrus sinensis x Citrus trifoliata


title: Illumina HiSeq 2500 (Citrus sinensis x Citrus trifoliata)

organism: Citrus sinensis x Citrus trifoliata


title: Illumina NextSeq 500 (Sarcophilus harrisii)

status: Public on Apr 05 2019

organism: Sarcophilus harrisii


title: Agilent Custom Mouse lncRNA (4*180K, Design ID:049801)

status: Public on Apr 07 2019

city: Beijing

first: jing

last: ouyang

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of microbiology, Chinese Academy of Sciences

organism: Mus musculus


title: Illumina NextSeq 500 (Siansivirga zeaxanthinifaciens CC-SAMT-1)

status: Public on Apr 15 2019


title: Illumina HiSeq 2500 (Aegilops speltoides)

organism: Aegilops speltoides


title: Illumina HiSeq 2500 (Aspidelaps lubricus cowlesi)

organism: Aspidelaps lubricus cowlesi


title: Illumina Genome Analyzer II (Dunaliella tertiolecta)

organism: Dunaliella tertiolecta


title: TaqMan Fluidigm 96 dynamic arrays

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

organism: Homo sapiens


title: Illumina NovaSeq 6000 (synthetic construct)

organism: synthetic construct


title: Illumina HiSeq 2000 (Pyricularia oryzae)

status: Public on Apr 03 2019

organism: Pyricularia oryzae


title: Illumina HiSeq 4000 (Escherichia coli W)

status: Public on Apr 04 2019

organism: Escherichia coli W


title: Illumina HiSeq 4000 (Cronobacter sakazakii)

organism: Cronobacter sakazakii


title: NNIIEM_Human_ApoArray_4х2k_v3.0

status: Public on Apr 02 2019

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

manufacturer: CustomArray Inc. CustomArray B3 Synthesizer


title: Illumina HiSeq 3000 (Human gammaherpesvirus 4)

organism: human gammaherpesvirus 4


title: BGISEQ-500 (Carex littledalei)

organism: Carex littledalei


title: Illumina HiSeq 2500 (Kluyveromyces marxianus)

organism: Kluyveromyces marxianus


title: Illumina HiSeq 2000 (Myzus persicae)

organism: Myzus persicae


title: Applied Biosystems Megaplex TaqMan Rodent MicroRNA Assay (Rodent Pool A)

status: Public on Apr 01 2019

city: Rozzano

first: Francesca

last: Ficara

state: MI

address: via Manzoni 56

country: Italy

institute: CNR/Istituto Clinico Humanitas

description: FAM-based qPCR assay.

first: Laura

last: Crisafulli

manufacture_protocol: See manufacturer's website.


title: Illumina HiSeq 2500 (Escherichia coli; Pseudomonas phage PP7)

organism:
Escherichia coli
Pseudomonas phage PP7


title: Illumina HiSeq 2000 (Moloney murine leukemia virus)

organism: Moloney murine leukemia virus


title: Agilent-066316 Rat CpG 2X400K

first: Yoon

last: Cho

address: hwarang-ro 14

institute: KIST

organism: Rattus norvegicus


title: Illumina NextSeq 500 (Aspidelaps lubricus cowlesi)


title: Agilent-037091 GGA_Campy_FineMapping

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

organism: Gallus gallus

description:
Arrays of this design have barcodes that begin with 16037091 or 2537091.
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 3000 ([Candida] glabrata)

organism: Nakaseomyces glabratus


title: Biomark high throughput Human miRNA RT-qPCR assay

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

description:
PCR assay
Biomark high throughput RT-qPCR assay
The plate was custom built for the RNAs. The instrument used was BioMark HD (Serial No: 90334). BioMark Data Collection Software version 4.1.3


title: Agilent-064853 Agilent_Rhesus 026806_and_custom_Cynomolgus genes (8x44k format)

city: Singapore

first: Sarah

last: Daud

address: 1E Kent Ridge Road,NUHS Tower Blk,Lvl 12,

country: Singapore

institute: National University of Singapore

organism: Macaca mulatta

description:
Customized Agilent Rhesus AMADID 026806 with custom genes. The microarray probes were designed using similar backbone from AMADID-026806 Macaca mulatta protein coding genes with additional customized probes from Macaca fascicularis coding genes related to natural killer cells. The cynomolgus probes added to this design have probeset ID that begins with CUST_. The updated content of the probes provide transcriptional coverage of distinct KIR genes associated with cynomolgus macaque KIR haplotypes.
Platform_description = Arrays of this design have barcodes that begin with 16064853 or 2564853.
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.

first: Makoto

last: Yawata

first: Siti

middle: S


title: NanoString nCounter Human Myeloid Innate Immunity Panel

status: Public on Aug 14 2017

city: Los Angeles

first: Suan-Sin

last: Foo

state: California

address: 1501 San Pablo St

department: Molecular Microbiology and Immunology

institute: University of Southern California

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


title: Illumina NextSeq 500 (Listeria monocytogenes)

last: GEO

organism: Listeria monocytogenes


title: Agilent-075606 MacFas_Refseq_mRNA_2015

status: Public on Apr 06 2019

city: hachiouji

first: yoshiyuki

last: ishii

address: takakura-cho

institute: Agilent

organism: Macaca fascicularis

description:
these probes are designed from NCBI Refseq 2015 May Macaca fascicularis protein coding genes.

Arrays of this design have barcodes that begin with 16075606 or 2575606.

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 (Cryptosporidium parvum)

organism: Cryptosporidium parvum


title: 3D-Gene Human Oligo chip 25k V2.2.0

status: Public on Sep 16 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

organism: Homo sapiens

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Takifugu fasciatus)

organism: Takifugu fasciatus


title: Illumina HiSeq 3000 (Pteropus alecto)

organism: Pteropus alecto


title: Illumina HiSeq 3000 (Eonycteris spelaea)

organism: Eonycteris spelaea


title: Illumina NextSeq 500 (Lasiodiplodia theobromae; Vitis vinifera)

organism:
Vitis vinifera
Lasiodiplodia theobromae


title: Illumina NextSeq 500 (Cryptosporidium parvum)


title: Agilent-084555 026652QM_RCUG_HomoSapiens (Probe Name Version)

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover


title: HiSeq X Ten (Brassica napus)

organism: Brassica napus


title: Agilent-084141 perche60k [Probe Name version]

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

organism: Perca fluviatilis


title: Exiqon miRCURY LNA™ microRNA Array [Cat# 208210-A; miRBase v.11.0]

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: miRCURY LNA™ microRNA Array ready-to-spot probe set 11.0 were purchased from EXIQON Cat#208210-A).Capture probes complementary to mature microRNAs for all microRNAs in human, mouse, rat and their related viruses registered in miRBase Release Version 11.0. The capture probes are Locked Nucleic Acid (LNA) enhanced oligonucleotides. All probes are Tm-normalized and amino modified.Dissolve the capture probes in 15 μL printing buffer resulting in a final concentration of 20 μM capture probe during spotting. The probes were then printed onto epoxy-coated slides (CEL Associates, Pearland, TX) with an OmniGrid 100 array (GeneMachine, San Carlos, CA) at 65% humidity and then incubated for 48 hours at the same humidity. Each slide contained three identical blocks in a landscape orientation. Within each block every probe was printed  in duplicates.


title: Taqman Low Density Array (TLDA) Human MicroRNA A Card (Catalog# 4398965)

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

description:
PCR assay
The 6 digit codes in the Platform IDs (e.g., 000377) represent Thermo Fisher's updated ordering numbers for the microRNA assays.  Please note that GPL17039 lists the outdated ordering numbers.


title: Illumina HiSeq 3000 (Cicer arietinum)

organism: Cicer arietinum


title: Illumina NovaSeq 6000 (Schistosoma mansoni)

organism: Schistosoma mansoni


title: Agilent-070156 Human_miRNA_V21.0_Microarray 046064 (Probe Name version)

status: Public on Mar 10 2016

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Human only version 21.0

Design creation details:
Created by: Agilent Technologies
Created Date:  10/06/2014

Design Format: 8 x 60K
Number of Distinct microRNA Targets Covered: 2549
Number of Agilent Controls: 2164

Arrays of this design have barcodes that begin with 16070156 or 2570156.

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


title: [HG-U219] Affymetrix Human Genome U219 Array [CDF: hgu219hsentrezgaltrabio162802]

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

relation: Alternative to: GPL13667 (Alternative CDF [official])


title: HiSeq X Ten (Sparassis latifolia)

status: Public on Apr 17 2019

organism: Sparassis latifolia