title: NanoString nCounter human fibrosis panel [NS_Hs_Fibrosis_V2.0+PLS_COVID_19_v2_C8240]

status: Public on Aug 25 2022

city: MADRID

first: José

last: Palacios

state: MADRID

address: CTRA COLMENAR VIEJO KM. 9.100

department: Pathology

country: Spain

institute: Hospital Universitario Ramón y Cajal

organism: Homo sapiens

technology: other

distribution: custom-commercial


title: Nanostring nCounter Elements TagSet [Custom Myeloid Gene Panel]

status: Public on Jul 10 2022

city: Cambridge

first: David

last: Mooney

state: MA

address: 58 Oxford Street

country: USA

institute: Harvard University

manufacturer: NanoString (tag oligos) and IDT (hybridization oliogs)

manufacture_protocol: followed manufactuer instructions - https://nanostring.com/wp-content/uploads/LBL-10241-04_nCounter_Elements_XT_User_Manual_EX-US.pdf


title: nCounter® Human v.3 miRNA expression platform

status: Public on Jun 30 2022

city: São Luís

first: Silma

middle: Regina

last: Pereira

state: Maranhão

address: Av. dos Portugueses, 1966, Bacanga

department: Department of Biology

country: Brazil

institute: Federal University of Maranhão


title: Custom-made human astrocyte RT-PCR array

status: Public on Jun 29 2022

city: New York

first: Limary

last: Cancel

state: NY

address: 160 Convent Ave

department: Biomedical Engineering

institute: The City College of New York

technology: RT-PCR

description:
Custom-made PCR assay panel
custom selection of neuroactive genes expressed in human astrocytes

distribution: non-commercial

manufacture_protocol: see manufacturer's website


title: BGISEQ-500 (Daphnia magna)

last: GEO

organism: Daphnia magna

technology: high-throughput sequencing

distribution: virtual


title: Nanostring nCounter GX Human Inflammation panel [NS_Infl_Hs_v2_C2534]

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


title: Sequel II (Venezuelan equine encephalitis virus (strain TC-83))

status: Public on Jun 28 2022


title: Microarrays of nuclearly encoded mouse tRNAs and supressor tRNA

status: Public on Apr 04 2023

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

organism: Mus musculus

technology: spotted oligonucleotide

manufacturer: Fraunhofer Institute for Biomedical Research (Potsdam, Germany)

manufacture_protocol:
1. Oligos were arrayed in 384 well plates with a final concentration of 10 µM in 3× SSC/0.01% SDS in a total volume of 25 µl.
2. Arrays were printed onto (3-Glycidyloxypropyl)trimethoxysilane (Sigma) activated glas slides using a contact-spotter (QArray 2, Moleculare Devices).
3. After spotting arrays were incubated overnight at 4°C in a humidified atmosphere and subsequently dried for 30 min at 30°C.
4. Arrays were stored in a dry atmosphere at room temperature until use.


title: Glucose metabolism RT profiler PCR array, PAHS 006Z, Qiagen, USA

city: Amman

first: Hamzeh

middle: J.

last: Al-Ameer

address: Madaba

department: Biology and Biotechnology

country: Jordan

institute: American University of Madaba

description: PCR assay


title: Illumina HiSeq 2500 (Trichoderma asperelloides)

status: Public on Jun 27 2022

organism: Trichoderma asperelloides


title: Illumina HiSeq 2500 (Bactericera cockerelli)

status: Public on Jun 24 2022

organism: Bactericera cockerelli


title: Qiagen Human Innate & Adaptive Immune Responses RT² Profiler PCR Array

city: London

first: Elena

last: Palma

state: -- US/Canada Only --

address: 111 Coldharbour Lane

country: United Kingdom

institute: The Roger Williams Institute of Hepatology

description: PCR assay


title: DNBSEQ-G400 (Lytechinus variegatus)

organism: Lytechinus variegatus


title: nCounter Mouse Immunology Panel

city: Chicago

first: Dulari

last: Jayawardena

state: Illinois

address: 820 S Damen Avenue, Rm 7221

department: Medicine

institute: University of Illinois at Chicago

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


title: HiSeq X Ten (Lupinus luteus)

organism: Lupinus luteus


title: Illumina HiSeq 2500 (Enterobacter cloacae complex)

organism: Enterobacter cloacae complex


title: Molecular Cartography Mouse 98 v3.0

status: Public on Oct 21 2022

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

technology: in situ oligonucleotide

manufacture_protocol: The probes for 98 genes were designed using Resolve’s proprietary design algorithm. Briefly, the probe-design was performed at the gene-level. For every targeted gene all full-length protein-coding transcript sequences from the ENSEMBL database were used as design targets if the isoform had the GENCODE annotation tag ‘basic’ (Frankish et al. 2019, Yates et al. 2020). To speed increase efficiency, the calculation of computationally expensive parts, especially the off-target searches, the selection of probe sequences was limited to sequences with high success rates. To filter highly repetitive regions, the abundance of k-mers was obtained from the background transcriptome using Jellyfish (Marçais & Kingsford 2011). Every target sequence was scanned once for all k-mers, and those regions with rare k-mers were preferred as seeds for full probe design. A probe candidate was generated by extending a seed sequence until a certain target stability was reached. A set of simple rules was applied to discard sequences that were found experimentally to cause problems. After these fast screens, every kept probe candidate was mapped to the background transcriptome using ThermonucleotideBLAST (Gans & Wolinsky 2008) and probes with stable off-target hits were discarded. Specific probes were then scored based on the number of on-target matches (isoforms), which were weighted by their associated APPRIS level (Rodriguez et al. 2017), favoring principal isoforms over others. A bonus was added if the binding-site was inside the protein-coding region. From the pool of accepted probes, the final set was composed by greedily picking the highest scoring probes.


title: GridION (Bos taurus)

organism: Bos taurus


title: MinION (Trypanosoma brucei)

organism: Trypanosoma brucei


title: Real-time quantitative PCR analysis Qiagen Rotor-Gene Q

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

description:
Real-time PCR cycler with 2 channels (green, yellow)
Real-time quantitative PCR analysis of NF-kB, TNFR1, BRAF, MEK and NRF2 genes in human D24, MM418-C1 melanoma and HaCaT cells


title: Illumina NextSeq 500 (Borreliella burgdorferi B31)

organism: Borreliella burgdorferi B31


title: TransStart Brassica juncea var. tumida RT-PCR AQ141-02

city: Chongqing

first: Zhaoming

last: Cai

state: Fuling

address: Juxian Road NO. 16 Fuling

country: China

institute: Yangtze Normal University

organism: Brassica juncea var. tumida

description: PCR assay


title: miRCURY LNA microRNA Array, 7th generation (mmu, miRBase 20)

city: Seoul

first: Bong-Kwang

last: Jung

address: 333 Hwagok-ro

country: South Korea

institute: Korea Association of Health Promotion

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Exiqon A/S, Skelstedet 16, 2950 Vedbaek, Denmark

manufacture_protocol: See Exiqon website


title: MinION (Venezuelan equine encephalitis virus (strain TC-83))


title: Illumina NovaSeq 6000 (Acanthamoeba castellanii; Campylobacter jejuni)

organism:
Campylobacter jejuni
Acanthamoeba castellanii


title: NextSeq 2000 (Xenopus laevis)

organism: Xenopus laevis


title: Illumina HiSeq 4000 (Stenotrophomonas maltophilia K279a)

status: Public on Jun 21 2022

organism: Stenotrophomonas maltophilia K279a


title: Illumina HiSeq 4000 (Cyclotella cryptica)

status: Public on Jun 22 2022

organism: Cyclotella cryptica


title: Illumina NovaSeq 6000 (Clostridium sp. AWRP)

status: Public on Jun 23 2022

organism: Clostridium sp. AWRP


title: Illumina NovaSeq 6000 (Aspergillus nidulans)

organism: Aspergillus nidulans


title: Illumina iSeq 100 (Zea mays)

organism: Zea mays


title: Illumina NovaSeq 6000 (Ustilago hordei)

organism: Ustilago hordei


title: Illumina NovaSeq 6000 (unidentified)

status: Public on Jun 20 2022

organism: unidentified


title: Illumina NextSeq 500 (Bacillus thuringiensis)

organism: Bacillus thuringiensis


title: Illumina HiSeq 2000 (Stenotrophomonas maltophilia K279a)


title: Illumina NovaSeq 6000 ([Clostridium] saccharolyticum WM1)

status: Public on Jun 18 2022

organism: [Clostridium] saccharolyticum WM1


title: NextSeq 2000 (Bacillus subtilis PY79)

organism: Bacillus subtilis PY79


title: DNBSEQ-G400 (Penicillium oxalicum)

organism: Penicillium oxalicum


title: Illumina NovaSeq 6000 (Spirodela polyrhiza)

organism: Spirodela polyrhiza


title: Proseek Multiplex OLINK Proteomics

status: Public on Jun 16 2022

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

organism: Homo sapiens

description: oligo labelled Ab


title: Illumina NovaSeq 6000 (Clostridium sporogenes ATCC 15579)

organism: Clostridium sporogenes ATCC 15579


title: Agilent-084674 Lactobacillus brevis microarray

status: Public on Jun 19 2022

city: Cork

first: Marine

last: Feyereisen

state: Cork

address: Western raod

country: Ireland

institute: Univeristy College Cork

organism: Levilactobacillus brevis

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


title: Illumina HiSeq 2000 (Dicosmoecus gilvipes)

status: Public on Jun 17 2022

organism: Dicosmoecus gilvipes


title: Illumina HiSeq 4000 (Monodelphis domestica)

organism: Monodelphis domestica


title: NextSeq 550 (Clostridium acetobutylicum; Escherichia coli)

organism:
Escherichia coli
Clostridium acetobutylicum


title: Illumina NovaSeq 6000 (Eriocheir sinensis)

organism: Eriocheir sinensis


title: NextSeq 550 (Methylomonas sp. DH-1)

status: Public on Jun 15 2022

organism: Methylomonas sp. DH-1


title: Illumina NovaSeq 6000 (Loxodonta africana)

status: Public on Jun 14 2022

organism: Loxodonta africana


title: Illumina NovaSeq 6000 (Orycteropus afer)

organism: Orycteropus afer


title: Illumina NovaSeq 6000 (Sarcophilus harrisii)

organism: Sarcophilus harrisii


title: Illumina NovaSeq 6000 (Methylomonas sp. DH-1)


title: Illumina NextSeq 500 (Sinorhizobium meliloti 2011)

organism: Sinorhizobium meliloti 2011


title: NextSeq 550 (Gossypium hirsutum)

organism: Gossypium hirsutum


title: Illumina HiSeq 4000 (Sarcophilus harrisii)


title: NextSeq 550 (Clostridium acetobutylicum)

organism: Clostridium acetobutylicum


title: Illumina MiSeq (Apilactobacillus kunkeei)

status: Public on Jun 13 2022

organism: Apilactobacillus kunkeei


title: BGISEQ-500 (Ideonella sakaiensis)

status: Public on Jun 10 2022

organism: Piscinibacter sakaiensis


title: Cytokine Profiling Antibody Array

status: Public on Jun 11 2022

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

institute: University of Ulsan College of Medicine

technology: antibody


title: Agilent-064079 Mustela putorius furo (ferret) array [Probe name version]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mustela putorius furo

description: Arrays of this design have barcodes that begin with 16064079 or 2564079.


title: Illumina HiSeq 2000 (Aechmea fasciata)

status: Public on Jun 09 2022

organism: Aechmea fasciata


title: Illumina HiSeq 4000 (Notamacropus eugenii)

organism: Notamacropus eugenii


title: Illumina NovaSeq 6000 (Halothece sp. PCC 7418)

organism: Halothece sp. PCC 7418


title: Illumina NextSeq 500 (Coprinopsis cinerea AmutBmut pab1-1)

organism: Coprinopsis cinerea AmutBmut pab1-1


title: NextSeq 550 (Hydra vulgaris)

status: Public on Jun 08 2022

organism: Hydra vulgaris


title: DNBSEQ-G400 (Halothece sp. PCC 7418)

status: Public on Jun 07 2022


title: Illumina NovaSeq 6000 (Populus trichocarpa)

organism: Populus trichocarpa


title: Illumina HiSeq 4000 (Orycteropus afer)


title: Illumina HiScanSQ (Danio rerio)

organism: Danio rerio


title: Illumina HiSeq 4000 (Loxodonta africana)


title: Agilent-064973 Mouse Min Custom CGH Microarray 20140306-2 G4126A (Feature Number version)

status: Public on Jun 06 2022

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: Research Institutes for Quantum Science and Technology

organism: Mus musculus

description:
SurePrint G3 Custom CGH Microarray, 8x60K, FeatureNumber version

Arrays of this design have barcodes that begin with 16064973 or 2564973

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 NovaSeq 6000 (Octopus bimaculoides)

status: Public on Jun 05 2022

organism: Octopus bimaculoides


title: Illumina HiSeq 2500 (Episyrphus balteatus)

organism: Episyrphus balteatus


title: Illumina NovaSeq 6000 (Apostichopus japonicus)

organism: Apostichopus japonicus


title: Illumina NovaSeq 6000 (Vibrio alginolyticus)

organism: Vibrio alginolyticus


title: Illumina HiSeq 2500 (Blattella germanica)

organism: Blattella germanica


title: Agilent-084783 Mus musculus array (circMouse_0410; Agilent Probe Name)

city: Hangzhou

first: Linlin

last: Wang

state: Zhejiang

address: Yuhangtang Road No.866

department: Department of Basic Medicine Sciences

institute: Zhejiang University

description:
Arrays of this design have barcodes that begin with 16084783 or 2584783.

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

The ID column represents the Agilent Probe Name.

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

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


title: Illumina HiSeq 4000 (Colletotrichum camelliae)

organism: Colletotrichum camelliae


title: Illumina HiSeq 2500 (Strigamia maritima)

organism: Strigamia maritima


title: Illumina HiSeq 2500 (Callorhinchus milii)

organism: Callorhinchus milii


title: Agilent-086294 Pseudomonas putida KT2440 array (Probe name version)

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

organism: Pseudomonas putida KT2440

description:
Arrays of this design have barcodes that begin with 16086294 or 2586294.

Orientation (086294_D_GEO_20200114.txt):
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Probe Name.

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

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


title: Illumina NovaSeq 6000 (Ananas comosus)

status: Public on Jun 03 2022

organism: Ananas comosus


title: Illumina NovaSeq 6000 (Bicyclus anynana)

status: Public on Jun 02 2022

organism: Bicyclus anynana


title: DNBSEQ-T7 (Xenopus laevis)

organism: Xenopus laevis


title: Illumina HiSeq 4000 (Eonycteris spelaea)

organism: Eonycteris spelaea


title: RT² Profiler™ PCR Array Mouse Cytokines & Chemokines

city: Washington, DC

first: Alexander

last: Kroemer

state: DC

address: 3800 Reservoir Road NW, Pasquerilla Healthcare Center (PHC), 2nd Floor,

department: Center for Translational Transplant Medicine (CTTM)

institute: MedStar Georgetown Transplant Institute

description:
Mouse Cytokines & Chemokines PCR panel
Qiagen RT² Profiler panel of PCR assays.

distribution: commercial


title: Illumina HiSeq 2000 (Synechococcus elongatus PCC 7942 = FACHB-805)

last: GEO


title: Illumina HiSeq 4000 (Phytophthora sojae strain P6497)

organism: Phytophthora sojae strain P6497


title: BGISEQ-500 (Phytophthora sojae strain P6497)


title: Qiagen RT² Profiler™ PCR Array Mouse Growth Factors PAMM-041Z

status: Public on Jun 01 2022

city: Ann Arbor

first: Nureen Hanisah

last: Mohamad Zaki

state: Michigan

address: 109 Zina Pitcher Pl, RM2438

department: Internal Medicine, GI

institute: University of Michigan


title: Illumina NovaSeq 6000 (Collinsella aerofaciens ATCC 25986)

status: Public on Jun 18 2022

organism: Collinsella aerofaciens ATCC 25986


title: Agilent-015061 pan-genomic C. elegans 4*44K microarray (Probe Name version)

city: PARIS

first: LINH CHI

last: BUI

address: 45 rue des Saints-Pères

department: INSERM

country: France

institute: Université de Paris

organism: Caenorhabditis elegans


title: Illumina HiSeq 2500 (Cloeon dipterum)

organism: Cloeon dipterum


title: Illumina NextSeq 500 (Bradyrhizobium diazoefficiens; Glycine max)

organism:
Glycine max
Bradyrhizobium diazoefficiens


title: nCounter Mouse Myeloid/Innate Immunity

status: Public on Jun 04 2022

city: Leuven

first: Johan

last: Van Weyenbergh

state: VL BR

address: Herestraat 49

department: Microbiology, Immunity and Transplantation

country: Belgium

institute: KU Leuven

organism: Mus musculus

manufacture_protocol: Mus musculus Myeloid/innate immunity panel as defined on nanostring.com


title: Mouse Immunology NanoString Probeset C2269

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine


title: Illumina NovaSeq 6000 (Pyricularia oryzae)

organism: Pyricularia oryzae


title: NanoString nCounter Human Myeloid Innate Immunity Panel v2 [NS_Hs_Myeloid_V2.0]

city: Oxford

first: Matthew

middle: J

last: Bottomley

state: Oxfordshire

address: Old Road Campus

department: Nuffield Department of Medicine

institute: University of Oxford

organism: Homo sapiens

manufacture_protocol: NanoString Technologies


title: Illumina NextSeq 500 (Drosophila melanogaster; Homo sapiens; Human alphaherpesvirus 1 strain 17)

organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1 strain 17


title: RPPA-Homo spaiens

status: Public on May 12 2021

city: Philadelphia

first: lei

last: guan

state: PA

address: 433 S University Ave.

department: Biology

institute: university of pennsylvania

technology: spotted peptide or protein

manufacturer: RPPA Core Facility, MD Anderson Cancer Center

manufacture_protocol: We stained slides for more than 400 unique antibodies and 3 secondary antibody negative controls which were analyzed on Array-Pro then by supercurve Rx64 3.1.1. There were 12 sets of replicated antibodies among slides. We performed QC test for each antibody staining (slide). The QC Score (Probability) values were also included in the data spreadsheet for your references. QC score above 0.8 indicates good antibody staining. We only included in the data for the all individual antibodies with QC Scores higher than 0.80 in the Heatmaps. In the case of antibodies with replicates, the one with the highest QC Score was used. For samples of tissue origin, we removed 7 antibodies cross react with damaged components (with unknown mechanism). There are 51 individual mouse antibodies (labeled -M) that will be removed for mouse tissue or xenograft samples, unless you specifically indicated for inclusion in your sample submission form.


title: NextSeq 2000 (Cuscuta campestris)

organism: Cuscuta campestris


title: Illumina NovaSeq 6000 (Culex quinquefasciatus)

status: Public on Jun 20 2022

organism: Culex quinquefasciatus


title: NextSeq 2000 (Caenorhabditis elegans)