title: DNBSEQ-T7 (Zea mays)

status: Public on Dec 31 2023

last: GEO

country: USA

organism: Zea mays

technology: high-throughput sequencing

distribution: virtual


title: B200H Candida albicans Eurogentec 14080k

city: Salamanca

first: Angel

last: Domínguez

state: Salamanca

address: Plaza de los Doctores de la Reina

department: Microbiology and Genetics/CIETUS/IBSAL

country: Spain

institute: University of Salamanca

organism: Candida albicans

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol: The development of Candida albicans DNA microarrays was carried out by Eurogentec in collaboration with the Galar Fungail European Consortium (http://www.pasteur.fr/recherche/unites/Galar Fungail/). These microarrays contain 6947 ORF’s represented by 60-bp primers. The oligonucleotide probes were synthesized using the standard phosphoramidite method. For reasons of compatibility with the slide surface, the linker C6-NH2 was added to all primers at their 5’ end. Microarrays were prepared by printing amino-modified long oligos on high quality glass slides using  a ChipWriterPro (ESII) robot (Bio-Rad). The arrayer used 32 pins to print DNA samples from 384-well microtiter plates onto glass slides. All the oligonucleotides were spotted as a duplicate and they were placed in area of 3.2 x 1.8 cm. The MicroArray contains 32 blocks and each block contains 416 dots. The distanced between spot to spot is ranging from 90 to 120 microns with 100 microns of spot diameter. The MicroArray includes serial dilution of Luciferase gene allowing to normalize the signal of hybridization and to evaluate the dynamic range of the scanners. For negative control three distinct oligonucleotides with 70, 50 and 30% identity of sequence with some highly expressed Yarrowia lipolytica genes, were incorporated to the MicroArray. This allows to evaluate the efficiency of hybridization and washing conditions.


title: Agilent-085718 Pfal_CACACA_plus_v1_Aug2018 [Feature Name version]

city: State College

first: Manuel

last: Llinás

state: Pennsylvania

address: W122 Millennium Science Complex, Pollock Road

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

organism: Plasmodium falciparum

technology: in situ oligonucleotide

description:
Genomic context PBM for CACACA motif in the Plasmodium falciparum genome.

Arrays of this design have barcodes that begin with 16085718 or 2585718.

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 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.

distribution: commercial

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


title: K060H Candida albicans Eurogentec 14080k


title: I180H Candida albicans Eurogentec 14080k


title: Illumina NovaSeq 6000 (Mus musculus domesticus x Mus musculus castaneus)

status: Public on Dec 28 2023


title: Illumina NovaSeq 6000 (Lethenteron reissneri)

organism: Lethenteron reissneri


title: PromethION (Bos grunniens x Bos taurus)

organism: Bos grunniens x Bos taurus


title: NextSeq 2000 (Escherichia coli K1)

organism: Escherichia coli K1


title: Utz Lab Mouse CTD Array

status: Public on Dec 29 2023

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

organism: Mus musculus

technology: spotted peptide or protein

distribution: non-commercial

manufacture_protocol: Antigens were conjugated to magnetic barcoded beads (MagPlex® Microspheres). In brief, unless stated otherwise, 8 ug of each antigen or control antibody was diluted in phosphate buffered saline (PBS) and transferred to 96-well plates. Diluted antigens and control antibodies were conjugated to 1×10^6 carboxylated magnetic beads per ID.


title: Agilent-026855 Mus musculus array [Probe Name version]

city: Frederick

first: Heekyong

middle: R

last: Bae

state: MD

address: Building 560, Room 31-23, NCI at Frederick

institute: National Cancer Institute

manufacture_protocol: see website


title: Agilent-074809 SurePrint G3 Mouse Gene Expression v2 8x60K Microarray [Gene-based version]

status: Public on Dec 27 2023

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

country: China

institute: Army Medical University

description: A different version of this platform with the Agilent Feature Number -or- Probe Name in the ID column is assigned accession number GPL21810 and GPL21163, respectively.


title: PromethION (Bos grunniens)

organism: Bos grunniens


title: Agilent-084453 human CBT_ceRNA400k_V1.0_20161103

status: Public on Dec 30 2023

city: Beijing

first: chuanjue

last: cui

address: No.167th Beilishi Road, Xicheng District

department: Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease,

institute: Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16084453 or 2584453.
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 LncRNA 12x135K Array V1.0 [2011-09-08_CB_human_expr]

first: Yujia

last: Wang

address: 22 Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description:
Human LncRNA Array V1.0 (12x135K, Roche Nimblegen, Mannheim, Germany). The array contains probes interrogating 30,618 lncRNAs collected from multiple authoritative databases, such as RefSeq, ENSEMBL, Chen Runsheng's Lab (Institute of Biophysics, Chinese Academy of Science) and other related literature.

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.

DESIGN_ID: 552471

manufacture_protocol: As described in CapitalBio Corporation Manual


title: HiSeq X Ten (Astragalus mongholicus)

organism: Astragalus mongholicus


title: HiSeq X Ten (Catharanthus roseus)

status: Public on Dec 26 2023

organism: Catharanthus roseus


title: Illumina NovaSeq 6000 (Trichophyton rubrum)

organism: Trichophyton rubrum


title: Illumina NovaSeq 6000 (Trichoderma harzianum)

organism: Trichoderma harzianum


title: Illumina HiSeq 4000 (Anopheles coluzzii)

status: Public on Dec 23 2023

organism: Anopheles coluzzii


title: HiSeq X Ten (Candida albicans; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Candida albicans


title: NextSeq 1000 (Sinorhizobium meliloti RU11/001)

status: Public on Dec 21 2023

organism: Sinorhizobium meliloti RU11/001


title: Illumina HiSeq 2500 (Dendrobium hybrid cultivar)

organism: Dendrobium hybrid cultivar


title: HiSeq X Ten (Astragalus membranaceus)

organism: Astragalus membranaceus


title: Agilent-085537 SurePrint G3 Custom GE 4x180K Microarray (Agilent, 9G4862A, 4×180K)

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

manufacture_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 1.65 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the slide. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.


title: Illumina NovaSeq 6000 (Lactiplantibacillus plantarum; Serratia marcescens)

organism:
Serratia marcescens
Lactiplantibacillus plantarum


title: Illumina NovaSeq 6000 (Streptomyces filamentosus)

organism: Streptomyces filamentosus


title: NextSeq 2000 (Mycobacterium tuberculosis variant bovis BCG)


title: Illumina NovaSeq 6000 (Mesembryanthemum crystallinum)

status: Public on Dec 20 2023

organism: Mesembryanthemum crystallinum


title: Illumina HiSeq 4000 (Dyadobacter sp.; Ensifer adhaerens; Neorhizobium tomejilense; Rhodococcus sp. (in: high G+C Gram-positive bacteria); Sinorhizobium meliloti; Sphingopyxis sp.; Variovorax beijingensis)

organism:
Sinorhizobium meliloti
Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Ensifer adhaerens
Sphingopyxis sp.
Dyadobacter sp.
Neorhizobium tomejilense
Variovorax beijingensis


title: DNBSEQ-G400 (Brassica napus)

status: Public on Dec 19 2023

organism: Brassica napus


title: Illumina NovaSeq 6000 (Bacteroides thetaiotaomicron VPI-5482)

organism: Bacteroides thetaiotaomicron VPI-5482


title: Illumina NovaSeq 6000 (Triticum aestivum; Zymoseptoria tritici)

organism:
Triticum aestivum
Zymoseptoria tritici


title: Illumina NovaSeq 6000 (Sepia officinalis)

organism: Sepia officinalis


title: MinION (Semliki Forest virus)

status: Public on Dec 18 2023

organism: Semliki Forest virus


title: Illumina NovaSeq 6000 (Semliki Forest virus)


title: DNBSEQ-G400 (Marchantia polymorpha)

organism: Marchantia polymorpha


title: NextSeq 2000 (Vibrio cholerae)

status: Public on Dec 17 2023

organism: Vibrio cholerae


title: Illumina HiSeq 2000 (Simonsiella muelleri)

organism: Simonsiella muelleri


title: Illumina HiSeq 2000 (Conchiformibius steedae DSM 2580)

organism: Conchiformibius steedae DSM 2580


title: Illumina HiSeq 2000 (Alysiella filiformis DSM 16848)

organism: Alysiella filiformis DSM 16848


title: Agilent-085948 MECP2_V3  G4125A

city: Houston

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16085948 or 2585948

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-086099 MECP2 ReReDesign  G4125A

description:
Arrays of this design have barcodes that begin with 16086099 or 2586099

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 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 NovaSeq 6000 (Ailuropoda melanoleuca)

status: Public on Dec 15 2023

organism: Ailuropoda melanoleuca


title: Illumina NovaSeq 6000 (Rhamphochromis sp. 'chilingali')

organism: Rhamphochromis sp. 'chilingali'


title: Illumina NovaSeq 6000 (Acinetobacter baumannii A118)

status: Public on Dec 14 2023

organism: Acinetobacter baumannii A118


title: NextSeq 1000 (synthetic construct)

organism: synthetic construct


title: Illumina HiSeq 3000 (Xenopus borealis)

organism: Xenopus borealis


title: Illumina NovaSeq 6000 (Stylophora pistillata)

organism: Stylophora pistillata


title: Illumina NextSeq 500 (Cannabis sativa)

organism: Cannabis sativa


title: PromethION (Capitella teleta)

organism: Capitella teleta


title: Illumina NextSeq 500 (Owenia fusiformis)

organism: Owenia fusiformis


title: Illumina NextSeq 500 (Dimorphilus gyrociliatus)

organism: Dimorphilus gyrociliatus


title: Illumina HiSeq 4000 (Owenia fusiformis)


title: Illumina NovaSeq 6000 (Candidatus Fervidibacter sacchari)

status: Public on Dec 11 2023

organism: Fervidibacter sacchari


title: Illumina NovaSeq 6000 (Delphinium anthriscifolium)

organism: Delphinium anthriscifolium


title: Illumina NovaSeq 6000 (Drosera capensis)

status: Public on Dec 10 2023

organism: Drosera capensis


title: [Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse [CDF: Brainarray ClariomSMouse_Mm_ENTREZG_23.0.0]

status: Public on Dec 13 2023

city: Paris

first: sebastien

last: jacques

address: 24 rue du faubourg saint jacques

department: Genomic

country: France

institute: Institut Cochin

organism: Mus musculus

description: The custom chip definition file from Brainarray Version 22.0  based on Entrez ID.

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


title: Illumina NovaSeq 6000 (Alternanthera philoxeroides)

status: Public on Dec 07 2023

organism: Alternanthera philoxeroides


title: nCounter Human v3 miRNA Expression Assay (NS_H_miR_v3b) panel

city: Bengaluru

last: Shankar

address: Mysore Rd, near City Market, New Tharagupet

department: Nephrology

country: India

institute: Institute of Nephrourology, Victoria Hospital Campus, Bengaluru

technology: other


title: RT PCR analysis of NF-kB, TNFR1, BRAF, MEK and NRF2 genes in human D24, MM418-C1 melanoma and HaCaT cells

city: Bundoora

first: Dao

last: Nguyen

state: Victoria

address: 289 McKimmies Rd

department: School of Science and Health and Biomedical Science

country: Australia

institute: Royal Melbourne Institute of Technology

technology: RT-PCR

description: Real-time PCR cycler with 2 channels (green, yellow)

manufacture_protocol: see manufacturer's website


title: Takara Zebrafish immune genes qPCR panel

status: Public on Dec 12 2023

city: Jeju

last: Shanaka

address: Ara-dong

department: Marine life Sciences

country: South Korea

institute: Jeju National University

organism: Danio rerio

description:
TP-951 J-1410 (catalog number)
PCR assay
RT-qPCR Dice™ TP950 Real-Time Thermal Cycler System (Takara, Japan)


title: Illumina NovaSeq 6000 (Saccharomyces cerevisiae S288C)

organism: Saccharomyces cerevisiae S288C


title: Illumina NovaSeq 6000 (Chiloscyllium plagiosum)

status: Public on Dec 06 2023

organism: Chiloscyllium plagiosum


title: DNBSEQ-T7 (Sulfolobus islandicus)

organism: Saccharolobus islandicus


title: DNBSEQ-G400 (Trypanosoma congolense)

organism: Trypanosoma congolense


title: DNBSEQ-T7 (Saccharomyces cerevisiae)

status: Public on Dec 05 2023

organism: Saccharomyces cerevisiae


title: Illumina HiSeq 2000 (Populus yunnanensis)

organism: Populus yunnanensis


title: Illumina NovaSeq 6000 (Candidatus Endoriftia persephone)

organism: Candidatus Endoriftia persephonae


title: nCounter® Breast Cancer 360™ Panel [GeneRLF: NS_BC_360_v2.0]

city: Indianapolis

first: Elizabeth

last: Yeh

state: Indiana

address: 635 Barnhill Drive, Medical Science Building A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

organism: Homo sapiens

description: Synthetic oligonucleotide pool corresponding to all panel gene targets used for normalization

manufacturer: NanoString Technologies™, Seattle, Washington, USA (776 genes total, 758 genes  + 18 reference genes)


title: Illumina NovaSeq 6000 (Amoebidium parasiticum)

status: Public on Dec 04 2023

organism: Amoebidium parasiticum


title: Illumina NovaSeq 6000 (Ichthyosporea sp. XGB-2017a)

organism: Ichthyosporea sp. XGB-2017a


title: Universal PBM 8x60k (Bulyk lab design)

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

organism: synthetic construct

manufacture_protocol: In situ oligosynthesized array with synthetic sequences that cover all possible 10-mers (Berger et al., Nature Biotechnology 2006). AMADID #030236


title: Illumina NovaSeq 6000 (Amoebidium appalachense)

organism: Amoebidium appalachense


title: Illumina NovaSeq 6000 (Sphaeroforma arctica)

organism: Sphaeroforma arctica


title: Arraystar Rat SmallRNA expression V1 Microarray

status: Public on Dec 02 2023

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Rattus norvegicus


title: Nanostring nCounter Human Metabolism Panel [NS_Hs_Metabolism_v1.0]

status: Public on Dec 01 2023

city: San Francisco

first: Saket

last: Jain

state: CA

address: 1450 3rd Street, HD 415

institute: University of California San Francisco


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene symbol version)

status: Public on Dec 31 2020

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University


title: Illumina HiSeq 2500 (Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S)

status: Public on Dec 08 2023

last: GEO


title: Agilent Whole Human Genome 44K

status: Public on Mar 06 2009

manufacture_protocol: Agilent's Sureprint 60-mer in situ


title: Illumina NovaSeq 6000 (Creolimax fragrantissima)

organism: Creolimax fragrantissima


title: BCM Reverse Phase Protein Array RPPA0016

status: Public on May 29 2018

description: While the tissue lysates were spotted on the slides, this platform includes the information on the antibodies used to assay these protein lysates.

manufacturer: Baylor College of Medicine Proteomics Core

manufacture_protocol: Protein lysates were prepared from PDX tumors with modified tissue protein extraction reagent (TPER; Pierce) and a cocktail of protease and phosphatase inhibitors (Roche Life Science). The lysates were diluted into 0.5 mg/mL of total protein in SDS sample buffer and denatured on the same day. The Aushon 2470 Arrayer (Aushon BioSystems) with a 40 pin (185 μm) configuration was used to spot samples and control lysates onto nitrocellulose-coated slides (Grace Bio-labs) using an array format of 960 lysates/slide (2880 spots/slide).   See also the PDF at the foot of this page.


title: NanoString VF_150921

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

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


title: SomaScan human discovery v4.1

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai