title: FZ_IBG1_4plex_041487

status: Public on Oct 09 2018

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

organism:
Gluconobacter oxydans
Escherichia coli
Corynebacterium glutamicum
Bacillus subtilis subsp. subtilis str. 168

technology: in situ oligonucleotide

distribution: custom-commercial

manufacturer: Agilent Technologies (Waldbronn, Germany)

manufacture_protocol: see Agilent Technologies


title: Agilent custom HK design array  v2[8mer]

status: Public on May 14 2018

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

country: USA

institute: NIH/NCI

organism: synthetic construct

description: 8mer sequence depicted below is not the sequence represented on the array, but the targeted sequence. Please see the two array design files attached below for array probe sequences.

manufacture_protocol: This protein binding microarray (PBM) involved binding GST-tagged proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.


title: NimbleGen Pine 12K array v1.0

status: Public on Dec 31 2017

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

organism: Pinus sylvestris

description: The probe sequences are available in the file: NimbleGen Pine 12K array v1.0.ndf.

manufacture_protocol: Propriety in situ oligonucleotide synthesis


title: Invitrogen ProtoArray ProtoArray

status: Public on Feb 26 2018

city: Boston

first: Suzanne

last: Walker

state: MA

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

organism: Homo sapiens

technology: spotted peptide or protein

description: Arrays from 3 different array batches are used in this study as described above in the description column of samples. Batches HA20358 (barcodes 74576-74579, 74581-74586, 74600, and 74617-74619), and HA20446 (barcodes 91384, 91412, and 91454) have identical test protein content arranged differently on the arrays, while HA20301 (barcodes 52630, 52641) has some differences in content. Content information is available on the basis of barcode on Invitrogen's website, and current batches of microarrays are available under catalog number PAH0525101

distribution: commercial

manufacture_protocol: Human proteins produced in insect cells are spotted in duplicate on a nitrocellulose glass slides in a 4x12 grid of subblocks, each of which includes several controls and test proteins in a 22x22 spot grid


title: Duke/RG_Elk1Ets1Gabpa_v1 (Agilent 4x180k)

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target Elk1/Ets1/Gabpa putative binding sites in genomic context.


title: Duke/RG_Runx1Runx2_v1 (Agilent 4x180k)

manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target Runx1/Runx2 putative binding sites in genomic context.


title: Agilent-075784 CapitalBio human circRNA Array V1.0 4x180K

status: Public on Feb 28 2018

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan


title: Agilent-061786 Pfal_Exome_Array (Exon-level version)

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 100 Galvin Life Science Building

department: Biological Science

institute: University of Notre Dame

organism: Plasmodium falciparum

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


title: Nimblegen Plasmodium falciparum 100813_LC_Pfal_5833_expr (locus tag version)

manufacture_protocol: High-density gene expression array manufactured by NimbleGen Inc using Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: CSIR SA Sorghum 4x44K v1.0

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

organism: Sorghum bicolor

distribution: non-commercial

manufacture_protocol: In-situ oligonucleotide synthesis, standard Agilent protocol.


title: Agilent-049690 Krill 2.0 [Probe Name]

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

organism: Euphausia superba

description:
Euphausia superba microarray

Arrays of this design have barcodes that begin with 16049690 or 2549690.

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.

"Nnnnn" accessions in the Platform represent the contig number of our krill 'master' transcriptome as described in Meyer et al (2015, PMID:25818178). One probe for each consensus sequence was designed to construct the custom high-density oligo DNA microarray platform. Probe design was carried out using the Agilent eArray Custom Microarray Design Service. Microarrays were synthesized in situ using the Agilent ink-jet technology with 8 x 60 K format. Microarray custom platform, named ?Krill 2.0? (eArray Design ID: 049690), showed 57,358 probes and 1,319 controls.


title: Illumina HiSeq 2500 (Oreoglanis setiger)

status: Public on Dec 28 2017

last: GEO

organism: Oreoglanis setiger

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2500 (Glyptothorax macromaculatus)

organism: Glyptothorax macromaculatus


title: Illumina HiSeq 2500 (Bagarius yarrelli)

organism: Bagarius yarrelli


title: Agilent-071199 Agbis_v1 040802

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

organism: Agaricus bisporus

description:
Arrays of this design have barcodes that begin with 16071199 or 2571199.

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 Human miRNA Expression Assay

status: Public on Dec 29 2017

city: Birmingham

first: Charitharth

last: Lal

state: AL

address: 619 South 19th Street

institute: University of Alabama at Birmingham

technology: other

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


title: HiSeq X Ten (Bubalus bubalis)

status: Public on Dec 27 2017

organism: Bubalus bubalis


title: Agilent-061786 Pfal_Exome_Array (Gene-level version)


title: Agilent custom HK design array [8mer]


title: Illumina HiSeq 4000 (Silurus lanzhouensis)

organism: Silurus lanzhouensis


title: Nimblegen Wyeomyia smithii custom Expression Array 12x135k [110623_Wye_ZL]

first: John

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

organism: Wyeomyia smithii

description:
This is a custom design whole transcriptome expression array in 12-plex format manufacture by Roche Nimblegen. Genes based on Wyeomyia smithii annotated draft transcriptome assembly are achived at NCBI  http://www.ncbi.nlm.nih.gov/under Bioproject, enter 259209. Accession: PRJNA259209. Entered 22 Aug 2014.

130,866 experimental probes:
Singleton are represented by single probes
Contigs are represented by 1-4 probes. Of the 21,279 unique contigs on the microarray:
21,000 contigs are represented by 4 probes
116 contigs are represented by 1 probe
85 contigs are represented by 2 probes
78 contigs are represented by 3 probes

BLAST hits and annotation for these sequences are available at: https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-015-1937-y/MediaObjects/12864_2015_1937_MOESM8_ESM.xlsx

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


title: Agilent-066702 Candida glabrata CBS138 array

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

organism: Nakaseomyces glabratus

description:
Agilent-066702 MH_C_glabrata_CBS138
Expression Microarray Analysis of  C. glabrata CBS138 under different environmental stressors.

Arrays of this design have barcodes that begin with 16066702 or 2566702.

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.

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


title: Qiagen Mouse Stem Cells RT2 Profiler Array [PAMM-405Z]

city: La Jolla

first: Aime

last: Lopez Aguilar

state: CA

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

organism: Mus musculus

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Candida Albicans Eurogentec 13440

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 DNA/cDNA

manufacture_protocol:
Construction of C. albicans Microarray
The C. albicans MicroArray has been developed in collaboration with the European Galar Fungail Consortium (www.pasteur.fr/recherche/unites/Galar_Fungail/). The Stanford Genome Technology Center generated the nucleotide sequence data for C. albicans with fundings from the NIDCR, NIH and the Burroughs Wellcome Fund. Information about coding sequences and proteins were obtained from the CandidaDB database: www.pasteur.fr/recherche/unites/Galar_Fungail/CandidaDB/, which has been developed by the Galar Fungail European Consortium. Specific primers were designed to amplify all 6039 putative ORFs. The primers were selected carefully to amplify only a specific region of each ORF. Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer. The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support. All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on 2 % agarose gels. Two independent probes per gene were selected to represent 34 genes. The MicroArray covers nearly 98 % of the annotated C. albicans genes and includes twelve mitochondrial genes, five intergenic regions, five S. cerevisiae genes and five genes for hybridization quality control, human glycerol-3-phosphate dehydrogenase and actin gene. We include in the MicroArray probes to evaluate the dynamic range of signal intensities, reverse transcription efficiency and spatial hybridization.
Spotting design
C. albicans MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For C. albicans MicroArray, we use simultaneously 32 pins to place the spots in area of 3.6 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 32 blocks, each containing 20 x 20 dots with 200 microns spacing center to center with a spot diameter of 100 microns.
MicroArray content
98 % of C. albicans genes were spotted twice in a single glass slide.
Tags (GFP, TAP, GST)
Marker genes Kan, Leu2, LacZ
Luciferase gene to spike mRNA samples
Negative controls (intergenic regions)
Cross hybridization S. cerevisiae genes having 70 %, 50 % and 30 % sequence identity with S. pombe genes
cDNA quality controls
Dynamic range controls
Spatial hybridization controls
Quality control
The C. albicans MicroArrays are certified to generate a high quality data.
All printed slides are previously selected for coating uniformity and low intrinsic background.
The MicroArrays are visually inspected for spotting quality (doughnuts), uniformity, integrity and for perfect alignment of spots and grids.
From each batch of printed MicroArray, three are randomly chosen for further quality control. We use the Terminal Transferase reaction to assess the amount of DNA covalently attached to the slides. Finally, we perform a real hybridization using labeled cDNA obtained from heat-choc cultured cells.


title: Illumina HiSeq 2000 (Erythranthe lewisii)

status: Public on Dec 26 2017

organism: Erythranthe lewisii


title: AB 5500 Genetic Analyzer (Solanum lycopersicum)

status: Public on Dec 21 2017

organism: Solanum lycopersicum


title: Illumina HiSeq 2000 (Blumeria graminis f. sp. secalis; Secale cereale)

organism:
Secale cereale
Blumeria graminis f. sp. secalis


title: Illumina HiSeq 2000 (Blumeria graminis f. sp. triticale; x Triticosecale)

organism:
x Triticosecale
Blumeria graminis f. sp. triticale


title: Illumina HiSeq 2000 (Scutellaria viscidula)

organism: Scutellaria viscidula


title: illumina HiSeq 2500 (Homo sapiens)

organism: Homo sapiens


title: Illumina HiSeq 4000 (Kluyveromyces wickerhamii)

organism: Kluyveromyces wickerhamii


title: Illumina HiSeq 2000 (Blumeria graminis f. sp. tritici; Triticum aestivum)

organism:
Triticum aestivum
Blumeria graminis f. sp. tritici


title: Illumina HiSeq 4000 (Kluyveromyces marxianus)

organism: Kluyveromyces marxianus


title: D14k3 Drosophila melanogaster array

city: Kiel

first: Christine

last: Fink

address: Am Botanischen Garten 1-9

department: Zoological Institute

institute: Kiel University

organism: Drosophila melanogaster

technology: spotted oligonucleotide

manufacturer: University Health Network Microarray Centre (www.microarrays,ca, Toronto, Canada)

manufacture_protocol: The arrays are printed on ChipWriter Pro (BioRad) using Stealth microarray printing pins (ArrayIT) on UltraGAPS microarray slides (Corning).


title: Illumina Infinium QC Array-24 (InfiniumQCArray-24v1-0_A3)

status: Public on Dec 20 2017

city: E Duarte Road

first: Javier

last: Ogembo

state: California

department: Experimental Therapeutics

institute: Beckman Research Institute of City of Hope

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 4000 (Kluyveromyces lactis x Kluyveromyces wickerhamii)


title: Illumina HiSeq 4000 (Kluyveromyces lactis x Kluyveromyces marxianus)


title: Ion Torrent Proton (Capra hircus)

organism: Capra hircus


title: Illumina HiSeq 4000 (Oncorhynchus mykiss)

status: Public on Dec 23 2017

organism: Oncorhynchus mykiss


title: Illumina HiSeq 2000 (Alligator mississippiensis)

organism: Alligator mississippiensis


title: Illumina HiSeq 2500 (Microcystis aeruginosa PCC 7806)

organism: Microcystis aeruginosa PCC 7806


title: Illumina HiSeq 2500 (Trametes versicolor)

status: Public on Dec 18 2017

organism: Trametes versicolor


title: Illumina HiSeq 2000 (Acropora cervicornis)

organism: Acropora cervicornis


title: Illumina HiSeq 2500 (Gloeophyllum trabeum)

organism: Gloeophyllum trabeum


title: Illumina HiSeq 2000 (Fusarium verticillioides; Zea mays)

organism:
Zea mays
Fusarium verticillioides


title: Human 40K B OciChip array

status: Public on Dec 19 2017

city: Rome

first: Silvia

last: Gioiosa

address: Via dei Tizii,6

department: Supercomputing Applications and Innovation

institute: CINECA

manufacture_protocol: See manufacturer’s website http://www3.ocimumbio.com/


title: Illumina HiSeq 4000 (Microhyla fissipes)

organism: Microhyla fissipes


title: Human 40K A OciChip array


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. D23580)

status: Public on Dec 14 2017


title: Shewanella baltica microarray 30k 1blk

status: Public on Dec 15 2017

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

institute: University of  Oklahoma

organism: Shewanella baltica

manufacture_protocol: Microarrays were made by a proprietary light-directed oligonucleotide synthesis method to synthesize 44-48 nucleotide long probes on glass slides. Probes were designed based on the genomes of Shewanella baltica OS185, OS195, OS223 and OS155.


title: Illumina HiSeq 2500 (Lynx rufus)

organism: Lynx rufus


title: ZB/SBS-NTU Plasmodium falciparum 3D7 11.0k v1.1

first: Margaret

middle: Jane

last: Mackinnon

country: Australia

organism: Plasmodium falciparum

manufacture_protocol:
Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.
The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: Qiagen Epithelial to Mesenchymal Transition RT² Profiler PCR Array [PAHS-090Z]

city: Erlangen

first: Pablo

last: Lindner

state: Bavaria

address: Universitaetsstr. 22

department: Pathology

institute: Universityclinic Erlangen

organism: Homo sapiens

description:
RT² Profiler PCR Array for PCR analysis
catalog number: PAHS-090Z


title: ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v1.2


title: Illumina HiSeq 2000 (Cornus officinalis)

organism: Cornus officinalis


title: Illumina HiSeq 2500 (Pleurotus ostreatus)

organism: Pleurotus ostreatus


title: [RaGene-2_0-st] Affymetrix Rat Gene 2.0 ST Array [ragene20st_Rn_ENTREZG ENTREZG_20]

status: Public on Dec 12 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

organism: Rattus norvegicus

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 4000 (Lynx rufus)


title: Illumina HiSeq 4000 (Equus caballus)

organism: Equus caballus


title: Illumina NextSeq 500 (Streptococcus pneumoniae D39)

status: Public on Dec 13 2017

organism: Streptococcus pneumoniae D39


title: Illumina HiSeq 2500 (Solenopsis invicta)

organism: Solenopsis invicta


title: ZB/SBS-NTU Plasmodium falciparum 3D7 IGR + ORF 16.4k v1.0


title: Illumina NextSeq 500 (Trichuris muris)

organism: Trichuris muris


title: Illumina HiScanSQ (Pseudotsuga menziesii)

status: Public on Dec 11 2017

organism: Pseudotsuga menziesii


title: Qiagen Epigenetic Chromatin Modification Enzymes RT² Profiler PCR Array  [PAHS-085Z]

description:
RT² Profiler PCR Array for PCR analysis
catalog number: PAHS-085Z


title: Valencia yeast v12

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

organism: Saccharomyces cerevisiae

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206 (PMID 15492934).


title: Illumina HiSeq 3000 (Sarcophilus harrisii)

organism: Sarcophilus harrisii


title: Illumina HiSeq 2000 (Galleria mellonella)

organism: Galleria mellonella


title: Illumina HiSeq 2500 (Rhizobium tropici)

organism: Rhizobium tropici


title: Illumina HiSeq 2000 (Actinidia chinensis)

organism: Actinidia chinensis


title: Illumina MiSeq (Sulfolobus acidocaldarius DSM 639)

organism: Sulfolobus acidocaldarius DSM 639


title: Illumina HiSeq 2500 (Homo sapiens; Influenza A virus (A/WSN/1933(H1N1)))

organism:
Homo sapiens
Influenza A virus (A/WSN/1933(H1N1))


title: Illumina HiSeq 2000 (Mycobacterium marinum)

status: Public on Dec 10 2017

organism: Mycobacterium marinum


title: Illumina HiSeq 4000 (Mycobacterium smegmatis str. MC2 155)

organism: Mycolicibacterium smegmatis MC2 155


title: Illumina HiSeq 2500 (Meliniomyces bicolor)

status: Public on Dec 08 2017

organism: Hyaloscypha bicolor


title: Illumina HiSeq 2500 (Clostridioides difficile R20291)

organism: Clostridioides difficile R20291


title: BGISEQ-500 (Glycine max)

organism: Glycine max


title: Illumina HiSeq 2500 (Boechera depauperata)

status: Public on Dec 07 2017

organism: Boechera depauperata


title: Illumina HiSeq 2500 (Lactococcus lactis subsp. cremoris)

organism: Lactococcus cremoris


title: Illumina HiSeq 2500 (Sulfolobus acidocaldarius DSM 639)


title: [Rice] Affymetrix Rice Genome Array

status: Public on May 05 2005

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Oryza sativa

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

This array contains probes to query 51,279 transcripts representing two rice cultivars, with approximately 48,564 japonica transcripts and 1,260 transcripts representing the indica cultivar.This array contains probes to query 51,279 transcripts representing two rice cultivars, with approximately 48,564 japonica transcripts and 1,260 transcripts representing the indica cultivar. This unique design was created within the Affymetrix GeneChip Consortia Program and provides scientists with a single array that can be used for the study of rice. High-quality sequence data were derived from GenBank mRNAs, TIGR gene predictions, and the International Rice Genome sequencing project. The arrays were designed using NCBI UniGene Build #52, (May 7, 2004) incorporating predicted genes from GenBank and the TIGR Os1 v2 data set. (ftp.tigr.org FASTA, 89.3 MB)

Annotations derived from Affymetrix CSV file dated 4/01/2005

relation: Affiliated with: GPL16106 (Alternative CDF [affyricechipalt.cdf])

relation: Alternative to: GPL18620 (Alternative custom CDF)

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Citrus japonica)

organism: Citrus japonica


title: Illumina HiSeq 2500 (Citrus clementina)

organism: Citrus x clementina


title: Applied Biosystems (Thermo Fisher) Macaca mulatta TaqMan miRNA Custom Array

status: Public on Dec 09 2017

city: Baltimore

first: Kenneth

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

organism: Macaca mulatta

manufacture_protocol: qRT-PCR TaqMan Low Density Array. See manufacturer's website: https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-assays/mirna-ncrna-taqman-assays/taqman-mirna-profiling-openarray.html


title: Illumina HiSeq 2000 (Begonia x semperflorens-cultorum)

last: GEO

organism: Begonia x semperflorens-cultorum


title: Agilent-025241 Bifidobacterium breve UCC2003 21 nt tiling array (Probe name version)

city: Cork

first: Francesca

last: Bottacini

address: Western Road

department: APC Microbiome Institute & School of Microbiology

country: Ireland

institute: University College Cork

organism: Bifidobacterium breve UCC2003

description:
chemican in situ oligonucleotide synthesis
UCC2003 21 nt sliding window tiling arrays
Custom 1 X 224K microarray design of B. breve UCC2003 with 21 sliding window probes designed across the forward and reverse strand
Arrays of this design have barcodes that begin with 16025241 or 2525241.

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.

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


title: MGX_Coffee_microarray_15K [PROBE NAME]

city: Montpellier

first: Thierry

last: JOET

address: 911 Avenue Agropolis

department: DIADE

country: France

institute: IRD (Institut de Recherche pour le Développement)

organism: Coffea arabica

description:
The Coffea Genome Oligo contains 15.580 70mers representing 15.580 genes.
The Coffea canephora long oligonucleotide set was designed and synthetized by Operon (Town, State) based on the SGN Coffee built II (15721 unigenes; http://solgenomics.net/ ). An amino linker was attached to the 5'-end of each oligonucleotide. The oligonucleotides, selected to limit secondary structure, have a melting temperature of 67 ± 3°C, length 65 ± 5 bases, GC content 43 ± 5 %. More than 98 % of the oligonucleotides were within 1000 bases from the 3'-end of the available gene sequence. For 195 unigenes, no adequate oligonucleotide could be designed and so correspond to "missing genes". BLAST alignments were performed to identify oligonucleotides that could cross-hybridize with other sequences of the SGN Coffee Built II. Three oligonucleotides (opCocaV10004674, opCocaV10014770, opCocaV10009077) cover more than one unigene. Finally out of 15522 oligonucleotides designed, there are 371 oligonucleotides which have > 70% of overall identity to another unigene and have a contiguous identical length of more than 20nt common to another unigene.
The set also includes 12 unique positive and 12 unique negative controls provided in 16 replicates in a 384-well plate.

manufacturer: design: Operon - Array : Montpellier GenomiX

manufacture_protocol:
Manufacturing microarrays
The Coffea Array were spotted using the Amersham Biosciences Lucidea Array spotter on epoxysilane-coated mirror glass slides (Genewave). Negative and positive control oligo were also printed into 24 different sectors of each slide. After printing, the slides were stored at room temperature in a dessicator.


title: Illumina NextSeq 500 (Clostridium acetobutylicum ATCC 824)

organism: Clostridium acetobutylicum ATCC 824


title: Illumina HiSeq 2000 (Populus euphratica)

organism: Populus euphratica


title: Drosophila tumor Microarray

status: Public on Dec 06 2017

city: new haven

first: Tian

last: Xu

state: CONNECTICUT

address: 295 congress ave

department: Genetics

institute: Yale school of medicine

organism: Drosophila melanogaster

manufacture_protocol: DNA microarrays were made using PCR fragments of approximately 95% of Drosophila genes, according to the Berkeley Drosophila Genome Project data. Slides were coated with polylysine, printed using a GeneMachines OmniGrid printer with DNA suspended in 3X SSC, and then postprocessed using a DCE protocol (Diehl et al., 2001, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC31299/)


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENSG_20.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

manufacture_protocol: see manufacturer's protocol


title: Illumina HiSeq 2500 (Microcystis aeruginosa KW)

organism: Microcystis aeruginosa KW


title: Illumina HiSeq 2500 (Triticum monococcum)

organism: Triticum monococcum


title: Illumina NextSeq 500 (Crassostrea gigas)

status: Public on Dec 05 2017

organism: Magallana gigas


title: Illumina HiSeq 4000 (Crassostrea gigas)


title: Illumina HiSeq 2500 (Litopenaeus vannamei)

organism: Penaeus vannamei


title: Illumina NextSeq 500 (Vitis vinifera)

organism: Vitis vinifera


title: Illumina HiSeq 3000 (Salmo salar)

organism: Salmo salar


title: Illumina HiSeq 2500 (Montastraea cavernosa)

status: Public on Dec 04 2017

organism: Montastraea cavernosa


title: Illumina HiSeq 2500 (Streptomyces coelicolor)

organism: Streptomyces coelicolor


title: Illumina HiSeq 4000 (Beta vulgaris)

status: Public on Dec 03 2017

organism: Beta vulgaris


title: RT² Profiler™ PCR Array Human Hedgehog Signaling Pathway

status: Public on Dec 01 2017

city: chiyodaku misakichou

first: Shoko

last: Onodera

state: Tokyo

department: biochemistry

country: Japan

institute: Tokyo Dental collage

description: PCR assay


title: Human MI Ready 49K Human Genomic Array

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description: 49K Human Genomic Array based on catalog number #HS1100.


title: Illumina HiSeq 2500 (Pezoloma ericae)

organism: Hyaloscypha hepaticicola


title: Illumina HiSeq 4000 (Escherichia coli K-12)

organism: Escherichia coli K-12


title: Illumina HiSeq 2500 (Brucella abortus)

organism: Brucella abortus


title: Agilent Rice Gene Expression  4x44k Array (AMADID: 064815)  designed  by Genotypic Technology Private Limited.

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: Oryza sativa


title: FibroChip Release 1

city: Saint-Genès-Champanelle

first: Sophie

last: Comtet-Marre

address: Centre Auvergne-Rhône-Alpes

institute: Université Clermont Auvergne, INRA

organism:
Bacteroides fragilis
Bacteroides thetaiotaomicron
Butyrivibrio fibrisolvens
Fibrobacter succinogenes
Xylanibacter ruminicola
Selenomonas ruminantium
Ruminococcus albus
Ruminococcus flavefaciens
Enterococcus faecium
Lactococcus lactis
Clostridium acetobutylicum
Clostridium cellulovorans
Clostridioides difficile
Acetivibrio thermocellus
Clostridium beijerinckii
Ruminiclostridium cellulolyticum
Levilactobacillus brevis
Limosilactobacillus fermentum
Bifidobacterium adolescentis
Cellulomonas fimi
Cellulomonas flavigena
Neocallimastix frontalis
Neocallimastix patriciarum
Piromyces communis
Bifidobacterium animalis
Bacteroides ovatus
Fibrobacter intestinalis
[Eubacterium] cellulosolvens
Bacteroides sp.
Pseudobacteroides cellulosolvens
Lachnospira eligens
Agathobacter rectalis
Ruminococcus sp.
Enterobacter sp.
Piromyces sp.
Epidinium caudatum
Eudiplodinium maggii
Polyplastron multivesiculatum
Orpinomyces joyonii
Piromyces rhizinflatus
Segatella bryantii
Piromyces sp. 'equi'
Roseburia intestinalis
Pseudobutyrivibrio xylanivorans
Butyrivibrio hungatei
Bifidobacterium longum
Acetivibrio clariflavus
Epidinium ecaudatum
Roseburia hominis
uncultured Neocallimastigales
Bacteroides xylanisolvens
Cellulosilyticum ruminicola
Ruminococcus champanellensis
Orpinomyces sp.

manufacture_protocol: see manufacturer's web site at https://www.genomics.agilent.com/en/Custom-Gene-Expression-Microarrays/Custom-Gene-Expression-Microarrays/?cid=AG-PT-132&tabId=AG-PR-1038


title: Illumina HiSeq 2000 (Monascus purpureus)

organism: Monascus purpureus


title: Agilent Custom Whole Genome Tomato 8x60K (AMADID: 065951) designed  by Genotypic Technology Private Limited.

organism: Solanum lycopersicum


title: Illumina HiSeq 2500 (Haloxylon ammodendron)

organism: Haloxylon ammodendron


title: Illumina HiSeq 3000 (Pseudomonas aeruginosa)

organism: Pseudomonas aeruginosa


title: Agilent-068651 MCCarmona v1

status: Public on Sep 11 2015

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

organism: Acinetobacter baumannii

description:
The assembly accession numbers (genomes@ncbi.nlm.nih.gov) are from NCBI:
LJHA00000000  Genome from A.baumannii 155 GEIH-2000 strain.
LJHB00000000  Genome from A.baumannii 105 GEIH-2010 strain.

Arrays of this design have barcodes that begin with 16068651 or 2568651.

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-052672 C. elegans Gene Expression 8x60k Array (AMADID: 052672) designed by Genotypic Technology Private Limited.

organism: Caenorhabditis elegans


title: Illumina HiSeq 2500 (Burkholderia cenocepacia H111)

status: Public on Feb 28 2017

organism: Burkholderia cenocepacia H111


title: Agilent-039596 Drosophila Gene Expression 8x60k Array (AMADID: 039596) designed by Genotypic Technology Private Limited.

organism: Drosophila melanogaster


title: Illumina HiSeq 1000 (Vitis amurensis)

organism: Vitis amurensis


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: huex10st_Hs_ENSG_20.0]

status: Public on Jun 02 2017

state: MD

organism: Homo sapiens

description:
Probe set data extracted from custom CDF;
huex10sthsensgcdf_18.0.0; Brainarray Version 20.0


title: Illumina MiSeq (Escherichia coli K-12)

status: Public on Sep 08 2014


title: MicroTOOLs_135K_oligo_v1.0

status: Public on Mar 07 2013

city: Santa Cruz

first: Irina

middle: N

last: Shilova

address: 1154 High str

department: Ocean Sciences

institute: UC Santa Cruz

organism: uncultured marine microorganism

first: Julie

last: Robidart

first: Harry

middle: J

last: Tripp

first: Kendra

last: Turk-Kubo

first: Boris

last: Wawrik

first: Mahdi

last: Belcaid

first: Shellie

last: Bench

first: Dreux

last: Chapell

first: Jackie

last: Collier

first: Chris

last: Francis

first: Scott

last: Gifford

first: Jana

last: Grote

first: Philip

last: Heller

first: James

middle: T

last: Hollibaugh

first: Bethany

last: Jenkins

last: LaRoche

first: Jonathan

last: Magasin

first: Andy

last: Millard

last: Moran

first: Annika

last: Mosier

first: Martin

last: Ostrowski

first: Ryan

last: Paerl

first: Micaela

last: Parker

first: Anton

last: Post

first: David

last: Scanlan

first: Holly

last: Simon

first: Mariya

last: Smit

first: Rhona

last: Stuart

first: Anne

middle: W

last: Thompson

first: Bess

last: Ward

first: Jody

last: Wright

first: Loui

last: Wurch

middle: P

last: Zehr

manufacture_protocol: Probe genes were selected using known molecular markers and metagenomic data, and oligonucleotide probes were designed using NimbleGen design software


title: Illumina HiSeq 2000 (Caenorhabditis japonica)

status: Public on Oct 05 2012

last: GEO

organism: Caenorhabditis japonica


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v18]

status: Public on Aug 22 2014

first: GEO

last: admin

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment.

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array


title: Agilent-046064 Unrestricted_Human_miRNA_V19.0_Microarray (Feature Number version)

status: Public on Dec 10 2013

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human only V19.0 design.

Arrays of this design have barcodes that begin with 16046064 or 2546064.

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.

relation: Alternative to: GPL18402 (miRNA ID version)

relation: Alternative to: GPL23860 (miRBase release 21 miRNA ID version)


title: NimbleGen Human Gene Expression 12x135K Array [100718_HG18_opt_expr]

status: Public on Jul 14 2014

description:
Designname: 100718_HG18_opt_expr
Designid: 535523
Build: HG18
FEAT_TYPE: transcript
Probe Length: 60mer
Target Genes: 45,033
Probes per Target: 3

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


title: Illumina HumanCytoSNP-12 v2.1 BeadChip

status: Public on Jul 06 2011

technology: oligonucleotide beads


title: [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array

status: Public on Apr 28 2005

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

The GeneChip® Mapping 100K Set is the first in a family of products for whole-genome association studies. It is comprised of a set of two arrays that enable genotyping of greater than 100,000 SNPs with a single primer.

copy number analysis
mean marker distance of 26 kb
provides both copy number and allele specific information


title: [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array


title: HiSeq X Ten (Danio rerio)

status: Public on Feb 21 2017

organism: Danio rerio


title: Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip

status: Public on Dec 02 2011

manufacture_protocol: see manufacturer's website