title: Pfizer BOLD Study TLDA Array

status: Public on Aug 30 2017

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

country: USA

institute: Pfizer

organism: Homo sapiens

technology: RT-PCR

description:
PCR assay
Custom TLDA array for the BOLD study.

distribution: virtual

manufacture_protocol: see manufacturer's website


title: ISB Halobacterium Spotted Microarray [gene-centered version using locus tags]

status: Public on Aug 31 2017

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

organism: Halobacterium salinarum NRC-1

technology: spotted oligonucleotide

description: Gene-centered version of platform GPL3739

distribution: non-commercial

manufacture_protocol:
MIAME platform type: spotted
MIAME availability: Arrays printed at ISB can be purchased, contact bmarzolf@systemsbiology.org for information.
Standard Operating Procedures for the Virtek(ESI) Spotter
*** Always remember that spotter pins are extremely fragile at the tips ***
To make spotter source plates:
1. Total volume should be 4-8 ul
2. Usually, DNA should be in 50% DMSO. This can be done most accurately be putting an appropriate amount of source material in spotting plates, then drying down with the speedvac and resuspending in the final volume of 3X SSC, 1.5M betaine.
Things not to do:
1. Move slides after printing starts ? just touching a slide can shift it and other slides enough to ruin the grid geometry.
2. Use air to blow dust off of slides - you could move the slides
3. Press the RED EMERGENCY button if it's not a emergency- this will turn off the spotter controller and abort the entire run
4. Use PCR products that have been purified, then dried down and resuspended in a very small volume, this is known to cause erratic surface tension and cause spots to run together.
When starting a new print run:
1. Allow blank slides to sit at 65% humidity for 24 hours
2. Renew sticky mat if it's dirty
3. Fill humidifier and turn on
4. Pull water out of water bath, wipe out bath and fill reservoir to get bath back to correct level- IT IS EXTREMELY IMPORTANT NOT TO OVERFILL THE WATERBATH OR SONICATOR BATH, WATER SHOULD BE JUST ABOVE THE POINT WHERE CUT RUNNING UP THE PIN ENDS
5. Place slides on the deck with label on the right-hand side. Secure slides by using spacer glass slides held in place with the magnets at the end of the platform.
6. Measure total X and Y distances spanned by slides, enter sizes under Calibration for Arraying->Slides
7. Print one dip with no source plate to ensure that pins are hitting all slides in the same plate (slight errors in Y direction especially can really throw off grid locations.)
8. Use the metal brace and spacer slides held by magnets to stabilize and line up the slides
9. Stabilize humidity at approximately 65%
10. Put blotting slide in place
To print slides:
1. Spin down 4 source plates at 2000 rpm for one minute
2. Put three remaining source plates (in order) at 4 C
3. Check blotting slide for blocked pins, change slide. Remove clogged/sticking pins and try to remedy by cleaning pin and/or printhead hole. If a pin isn't spotting on the blotter, it may just not be contacting the blotter.see if it's been spotting on actual slides.
4. Change water bath water at beginning of run.
5. Check level of water reservoir and sonicator bath- add water if necessary
6. Check humidity
7. Double-check orientation and number of source plate
8. Press operator button
9. Re-seal old plate and put in cold room
10. Set timer
11. Check old plate out, new plate in on printing checklist
When finished printing for the day:
1. Seal all plates and place in cold room
2. Turn off Spotter light
3. Turn monitor off
4. Leave computer ON
When finished with entire printing:
1. Allow spotter humidity to slowly drop and slides dry out.
2. Remove slides and place into plastic Telechem slide boxes.
3. Turn off Spotter light
4. Turn off fan/humidifier
5. Place boxes in desiccator at least 12 hours.
6. Blow off slides in boxes, then bake at 85 C for 2 hours.
7. Etch numbers and corners on slides (corners on back side), blow dry and place in desiccator ready for prehyb.
Things to do periodically:
1. Just keep an eye on the slides themselves to see if the grids are being formed as expected
To clean a clogged pin:
1. Remove pin by pulling out from top with a small forceps.
2. Dip in water and blow dry with air tip, repeatedly if necessary.
3. Make sure water reservoir is sufficiently full - low water often causes clogging.
Random experiments that we have tried and their results:
1. Effect of Temperature and Humidity on Spot Size
Printed H-70 in 3X SSC onto Telechem Amine slides. Temperatures chosen were 18 C, 20 C, 22 C, and humidities of 40%, 50%, 60% resulting in 9 different conditions. Hybridization was with labeled PCR primer for 3 hours.
Results: Differences were seen in specific grids, but grid-grid variability was too high to establish a conclusive pattern. Spots generally were most intense in a 90-100 micron diameter, then had a lighter halo that could extend to 130-150 microns. It appeared that Halo size was often smallest at 18 C, 130-140 microns. We decided to print at ambient temperature, generally 18-20 C.
2. Effect of Volume and Humidity on Maximum Spots per Dip
Pooled 96 wells of purified PCR product and added SSC for a final concentration of 3X. Then set up a plate so that 8 pins would print 1ul, another 8 would print 2ul, 4ul, 6ul, 8ul and 10ul. This 48-pin dip was then printed 25 spots in the Y direction, across 10 plain glass slides for a total of 250 spots. This print was done with increasing indent at 75%, 70%, 65%, 60% and 55% humidity.
Results: At 1-2ul, pins ran out of juice at 25-50 spots at all humidities. At 4ul, 200-225 spots could be printed at 65% or higher humidity. With 6ul or more, 250 spots could be printed at 65% or higher humidity. Based upon this, we chose 65% humidity for all printing.


title: Illumina HiSeq 2500 (Capsella orientalis)

status: Public on Aug 28 2017

last: GEO

organism: Capsella orientalis

technology: high-throughput sequencing


status: Public on Jan 31 2018

city: Utrecht

first: Michael

last: VanInsberghe

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: The Hansen microfluidic variability human miR-17-5p platform measures amplification uniformity across a microfluidic RT-qPCR array

first: Hans

last: Zahn

first: Adam

last: White

first: Oleh

middle: I

last: Petriv

first: Carl

middle: L

last: Hansen


title: Illumina NextSeq 500 (Acinetobacter baumannii)

status: Public on Aug 29 2017

organism: Acinetobacter baumannii


title: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [HuGene21st_Hs_ENTREZG_20.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: in situ oligonucleotide

description:
Brainarray: HuGene21st_Hs_ENTREZG_20.0.0
http://mbni.org/customcdf/20.0.0/entrezg.download/hugene21st_Hs_ENTREZG_20.0.0.zip

distribution: custom-commercial

relation: Alternative to: GPL17692 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: IMMKH Mhominis 15K v1.0

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

organism: Metamycoplasma hominis

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


title: Illumina HiSeq 2500 (Mycobacterium sp. PH-06)

status: Public on Aug 23 2017

organism: Mycobacterium dioxanotrophicus


organism:
Homo sapiens
Mus musculus

description: The Hansen microfluidic human mouse microRNA platform measures the expression of 19 miRNA and one snoRNA in single cells


title: Hansen microfluidic human mRNA

description: The Hansen microfluidic human endogenous mRNA platform measures the expression of commonly used endogenous reference genes (TBP, GAPDH, RPPH1), and genes of interest (ABL1, GGCX), and a negative control (Mmu Gapdh) single cells


title: Agilent-049943 mosquito array [probe name version]

status: Public on Aug 25 2017

city: Berlin

first: Lena

last: Lampe

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

organism:
Tribolium castaneum
Bombyx mori
Aedes aegypti
Anopheles gambiae
Culex quinquefasciatus
Drosophila melanogaster
Apis mellifera

description: Custom mosquito array containing probes of novel Anopheles gambiae miRNA and other insects


title: [MoGene-2_1-st] Affymetrix Mouse Gene 2.1 ST Array [CDF: mogene21st_Mm_ENTREZG_21.0.0]

organism: Mus musculus

description: This array is identical to GPL17400 but the data were analyzed with a custom CDF environment.

relation: Alternative to: GPL17400 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


description: The Hansen microfluidic variability human GAPDH platform measures amplification uniformity across a microfluidic RT-qPCR array


title: [Axiom_TSB_JPA1] Affymetrix Axiom® TSB_JPA1 Japonica Array Ver 1

status: Public on Aug 22 2017

city: Sendai

first: Yoichi

last: Kakuta

state: Miyagi

address: 1-1 Seiryo Aoba

country: Japan

institute: Tohoku University


title: GE Healthcare/Amersham Biosciences CodeLink Rat Whole Genome Bioarray LAYOUT EXP287X128-950.22.ID (Probe_name version)

city: Sao Paulo

first: Vinicius

last: Bassaneze

state: SP

address: Av. Dr. Eneas de Carvalho Aguiar, 44

department: Cardiopneumology

country: Brazil

institute: Heart Institute

organism: Rattus norvegicus

manufacture_protocol: see manufacturere's website


title: Illumina HiSeq 2000 (Capsella orientalis)


title: Illumina HiSeq 2000 (Mycobacterium smegmatis str. MC2 155)

organism: Mycolicibacterium smegmatis MC2 155


title: Illumina HiSeq 2500 (Crocus sativus)

organism: Crocus sativus


title: Illumina HiSeq 2500 (Capsella grandiflora)

organism: Capsella grandiflora


title: Illumina HiSeq 2500 (Tetrahymena thermophila)

organism: Tetrahymena thermophila


title: Agilent.SingleColor.36575, Commercial Zebrafish, 8x 60k, 60mer Microarray

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

organism: Danio rerio


title: Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)

status: Public on Aug 27 2017


title: Agilent-061231 Custom Salmonella GE 8x15k Microarray [ProbeName version]

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344


title: Illumina HiSeq 2500 (Mus musculus; Toxoplasma gondii)

organism:
Toxoplasma gondii
Mus musculus


title: Agilent-045525 Bifidobacterium array [Gene-level version]

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

organism:
Bifidobacterium adolescentis
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Bifidobacterium bifidum PRL2010
Bifidobacterium breve 12L

description: Array contains 4 Bifidobacterium species


title: Agilent-075764 Synechocystis sp. PCC 6803 array (Feature number version)

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

organism: Synechocystis sp. PCC 6803

description: The ID column represents the Agilent Feature Extraction feature number.


title: Illumina MiSeq (Myxococcus xanthus)

status: Public on Aug 16 2017

organism: Myxococcus xanthus


title: Illumina HiSeq 2500 (Acidipropionibacterium acidipropionici)

organism: Acidipropionibacterium acidipropionici


title: Illumina NextSeq 500 (Coryphaena hippurus)

organism: Coryphaena hippurus


title: Illumina HiSeq 2000 (Acinetobacter baumannii ATCC 17978)

organism: Acinetobacter baumannii ATCC 17978


title: Agilent-033142 Pseudomonas putida NBAII-RPF9 8x15K array (Probe name version)

city: Bangalore

first: Rajagopal

last: Rangeshwaran

state: Karnataka

address: Bellary Road

department: Molecular Entomology

country: India

institute: National Bureau of Agricutural Insect resource

organism: Pseudomonas putida

manufacture_protocol: see manufacturer's website www.agilent.com/chem/feprotocols.


title: Illumina MiniSeq (Mus musculus)


title: Illumina NextSeq 500 (Plasmodium knowlesi)

status: Public on Aug 15 2017

organism: Plasmodium knowlesi


title: Illumina HiSeq 4000 (Arachis hypogaea)

status: Public on Aug 17 2017

organism: Arachis hypogaea


title: STREM platform (Stress Response Microarray in Mytilussp)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

organism:
Mytilus californianus
Mytilus edulis
Mytilus galloprovincialis
Magallana gigas

manufacture_protocol: STREM platform was constructed arraying on glass slides 465 DNA oligo  corresponding to the 3’-portion of a set of 16 biological processesat cellular:  Lysosomal activity, DNA Metabolism, Translation, Mitochondrial activity, Carbohydrate metabolism, Heat choc response, Oxydatif stress, Proteolysis, Phase I and II detoxification, Metal resistance, Endocrine disruptors, Endocytosis,  Macrophage, Pumps, Cytoskeleton and  Adhesion to substrate. The probes are triplicated randomly to fill a 1395-feature sub-microarray for a total of 8 sub-arrays per slide.  All sequences are from Mytilus californianus,  galloprovincialis, edulis and CrassosteraGigas . Spotting was performed using the robotic system Genpak Array 21 (Genetix, Hampshire, UK) equipped with 6 Stealth Micro Spotting Pins SMP 3B (ArrayIt) settled to obtain spots with an average diameter of 90 µm.  Spotting was performed at 50% relative humidity to obtain the best spot morphology and to reduce the plate evaporation. Microarrays were then processed in a UV cross linker (Stratagene, La Jolla, CA, USA) (total power of 300 mJoules) for the binding the DNA to the slides. Microarrays were finally processed to remove any unbound product, dried and stored under vacuum at room temperature in sealed boxes.


title: Illumina NextSeq 500 (Plasmodium yoelii)

last: GEO

organism: Plasmodium yoelii


title: Illumina HiSeq 4000 (Jatropha curcas)

status: Public on Aug 21 2017

organism: Jatropha curcas


title: Illumina HiSeq 2500 (Leishmania infantum)

organism: Leishmania infantum


title: Agilent-063470 Chrysanthemum morifolium EST Array [probe name version]

status: Public on Aug 19 2017

city: Tsukuba

first: Akemi

last: Ohmiya

state: Ibaraki

address: Fujimoto 2-1

department: Institute of Vegetable and Floriculture Science

institute: National Agriculture and Food Research Organization

organism: Chrysanthemum x morifolium

description:
Arrays of this design have barcodes that begin with 16084984 or 2584984.

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 Names.


title: Illumina MiSeq (Novosphingobium resinovorum)

status: Public on Aug 14 2017

organism: Novosphingobium resinovorum


title: Illumina HiSeq 2000 (Trichophyton rubrum)

organism: Trichophyton rubrum


title: Illumina NextSeq 500 (Plasmodium chabaudi)

organism: Plasmodium chabaudi


title: Illumina NextSeq 500 (Plasmodium vivax)

organism: Plasmodium vivax


title: Illumina HiSeq 2000 (Escherichia coli DH1)

organism: Escherichia coli DH1


title: Illumina HiSeq 2500 (Penicillium citrinum)

organism: Penicillium citrinum


title: Illumina HiSeq 2000 (Phaeocystis antarctica)

organism: Phaeocystis antarctica


title: Illumina HiSeq 2000 (Oncorhynchus gorbuscha)

organism: Oncorhynchus gorbuscha


title: Exiqon, miRCURY LNA microRNA array, 6th gen (hsa, mirbase 17, Gene ID version)

status: Public on Aug 12 2017

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: Section 7641

country: Denmark

institute: Rigshospitalet

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Saimiriine gammaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: Herpesvirus saimiri strain A11

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

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: HiSeq X Ten (Saccharomyces cerevisiae BY4741)

status: Public on Aug 10 2017

organism: Saccharomyces cerevisiae BY4741


title: Illumina NextSeq 500 (Drosophila sechellia)

status: Public on Aug 09 2017

organism: Drosophila sechellia


title: Illumina HiSeq 2500 (Camelina sativa)

organism: Camelina sativa


title: Illumina HiSeq 2500 (Medicago truncatula)

status: Public on Aug 11 2017

organism: Medicago truncatula


title: Illumina HiSeq 2500 (Solanum lycopersicum x Solanum habrochaites)

status: Public on Aug 08 2017


title: Illumina HiSeq 2000 (Pectobacterium carotovorum subsp. brasiliensis PBR1692)

organism: Pectobacterium brasiliense PBR1692


title: Illumina HiSeq 3000 (Homo sapiens; Human gammaherpesvirus 8)

organism:
Homo sapiens
Human gammaherpesvirus 8


title: Illumina HiSeq 2500 (Homo sapiens; Human alphaherpesvirus 1)

organism:
Homo sapiens
Human alphaherpesvirus 1


title: Illumina NextSeq 500 (Nautella italica)

organism: Phaeobacter italicus


title: Illumina NextSeq 500 (Drosophila erecta)

organism: Drosophila erecta


title: Illumina HiSeq 2500 (Solanum habrochaites)

organism: Solanum habrochaites


title: Illumina NextSeq 500 (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: microRNA Ready-to-Use PCR, Human panel I+II, V4.R

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

organism: Homo sapiens

manufacture_protocol: see manufacturer's website (http://www.exiqon.com/mirna-pcr-panels)


title: Illumina NextSeq 500 (Drosophila persimilis)

organism: Drosophila persimilis


title: Illumina HiSeq 2500 (Pteropus alecto)

status: Public on Aug 07 2017

organism: Pteropus alecto


title: Illumina HiSeq 4000 (Artemisia argyi)

organism: Artemisia argyi


title: Fluidigm SNP genotyping

city: Ames

first: Maria

middle: Guadalupe

last: Salas Fernandez

state: IA

address: 1126E Agronomy Hall

department: Agronomy

institute: Iowa State University

organism: Sorghum bicolor

technology: other

description:
98 SNPtype Assays were designed via Fluidigm, and 82 SNPs were succefully genotyped using 4 X 96.96 Dynamic Array™ IFCs in total 359 samples.
GenBank assembly accession:   GCA_000003195.3 (latest)   RefSeq assembly accession:   GCF_000003195.3 (latest)
SNPtype/Taqman genotyping


title: [FDA-LM2s521098] Custom Affymetrix Listeria GeneAtlas Array Strip

status: Public on Aug 03 2017

city: Laurel

first: Atin

last: Datta

address: 8301 Muirkirk Rd

department: CFSAN/DVA

institute: FDA

organism: Listeria monocytogenes


title: Illumina NextSeq 500 (Drosophila simulans)

organism: Drosophila simulans


title: TaqMan Low Density Array (TLDA, v2.0), catalog 4444913

city: Boston

first: Anurag

last: Singh

address: 72 E. Concord St.

department: Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

description:
PCR assay
Taqman assay array to quantitate 384 microRNAs by qPCR


title: NanoString nCounter Human miRNA Expression Assay v1.6

status: Public on Aug 04 2017

city: Rockville

first: Khadijah

last: Mitchell

address: 37 Convent Drive, Building 37, Room 3060

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

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


title: LC Sciences Beta macrocarpa miRNA array

city: Beijing

first: Junying

last: Liu

state: Beijing

address: yuan ming yuan weat road

department: Plant Pathology

country: China

institute: China Agricultural University

organism: Beta macrocarpa

description: Probe names that include "PC-" represent novel B. macrocarpa miRNAs.

manufacture_protocol: See manufacturer's website


title: Exiqon miRCURY LNA microRNA array, 6th generation [miRBase v16, Probe_ID version]

city: Nanjing

first: Yabing

last: Chen

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu

institute: Nanjing University

organism: Mus musculus


title: Illumina HiSeq 3000 (Dermatophagoides pteronyssinus)

organism: Dermatophagoides pteronyssinus


title: Illumina HiSeq 2500 (Plasmodium berghei ANKA)

status: Public on Aug 02 2017

organism: Plasmodium berghei ANKA


title: Illumina NextSeq 500 (Drosophila melanogaster x Drosophila simulans)


title: Exiqon miRCURY LNA Universal RT microRNA PCR Human Panel I

city: Stockholm

first: Fernanda

last: Costa Svedman

address: Solnavägen 1

country: Sweden

institute: Karolinska Institute

manufacture_protocol: See manufacturer's website.


title: JCVI PFGRC Trypanosoma brucei 37K v2 array designed primarily based on strain TREU927

status: Public on Aug 01 2017

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

organism: Trypanosoma brucei brucei TREU927

description: This set includes 8381 oligonucleotides, has 37632 spots distributed in 48 blocks.

manufacture_protocol: 2QTB, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Illumina MiSeq (Human immunodeficiency virus 1)

organism: Human immunodeficiency virus 1


title: Agilent-046064 Unrestricted_Human_miRNA_V19.0_Microarray (miRBase release 21 miRNA ID version; Grid date: 06-Oct-2014)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

distribution: commercial

relation: Alternative to: GPL18044 (Feature Number version)

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


title: Illumina HiSeq 2500 (Allium sativum)

organism: Allium sativum


title: Illumina HiSeq 4000 (Macaca mulatta)

status: Public on Aug 24 2017

organism: Macaca mulatta


title: Ion Torrent Proton (Bacillus subtilis)

organism: Bacillus subtilis


title: Illumina HiSeq 3000 (Rattus norvegicus)

status: Public on Aug 22 2017

organism: Rattus norvegicus


title: Illumina HiSeq 1500 (Branchiostoma lanceolatum)

organism: Branchiostoma lanceolatum


title: nCounter Mouse Immunology V1 (Customized for Saa1/2)

city: New York

first: Thomas

middle: W

last: Battaglia

state: NY

address: 423 E 23rd Street

department: Medicine

institute: NYU School of Medicine

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


title: Illumina HiSeq 2500 (Drosophila melanogaster x Drosophila simulans)


title: Olea_BOleae_v1

status: Public on May 06 2017

city: Rende

first: Fabrizio

last: Carbone

state: CS

address: C.da Li Rocchi Vermicelli

department: Research Centre for Olive, Citrus and Tree Fruit

institute: Council for Agricultural Research and Economics (CREA)

organism: Olea europaea

manufacture_protocol: Probes were synthesized via in situ on chips based on CustomArrayTM semiconductor technology by using a CustomArrayTM Synthesizer (CustomArray Inc., Bothell, WA, USA).


title: JCVI PFGRC Trypanosoma brucei 19K v3 array designed primarily based on strain TREU927

description: This set includes 8375 oligonucleotides, has 19200 spots distributed in 48 blocks.

manufacture_protocol: 3QTB, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Illumina HiSeq 4000 (Camellia japonica)

organism: Camellia japonica


title: Agilent-038045 Candida albicans 4X180K array (Probe name version)

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

organism: Candida albicans


title: HiSeq X Ten (Oryza sativa Japonica Group)

last: GEO

organism: Oryza sativa Japonica Group


title: Applied Biosystems Taqman miRNA

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

description: qPCR array

manufacture_protocol: see manufacturer's website


title: Agilent-017150 UCC L.salivarius UCC118 45K (Feature Number version)

city: Cork

first: Denise

middle: B

last: Lynch

state: Not Applicable

address: College Road

department: APC Microbiome Institute

country: Ireland

institute: University College Dublin

organism: Ligilactobacillus salivarius UCC118


title: Phalanx Biotech Mouse OneArray Plus

city: Chicago

first: Christopher

middle: Robert

last: Manzella

state: IL

address: 820 S. Damen Ave.

institute: University of Illinois at Chicago

manufacture_protocol: See Phalanx Biotech website


title: Agilent-069636 Salamandra salamandra  Microarray (GeneName version)

status: Public on Jul 06 2017

city: Braunschweig

first: Daniel

last: Goedbloed

address: Mendelssohnstrasse 4

institute: TUBS

organism: Salamandra salamandra

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


title: CapitalBio custom Human LncRNA array

city: Guangzhou

first: Rui

last: Xu

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-Sen University Cancer Center

organism: Homo sapiens

manufacturer: State Key Laboratory of Oncology in South China,Sun Yat-sen University

manufacture_protocol: Probe: synthesized by Invitrogen (Shanghai, China).  Microarray process: The microarray fabrication process in house was described in our previous study (Wang HY, Luo M, et.ct, Genome Res 2005;15:276-283) except for the printing by a SmartArrayTM -136 printer (CapitalBio Inc., Beijing, China).  Spotting protocol: Every probe was printed twice on the glass.  5040 spots were printed in 12 blocks. There were 420 spots in every block, including 402 spots for 201 lncRNA probes, and other 18 spots for 3 internal controls, 2 external controls, 3 negative controls.


title: Illumina HiSeq 2000 (Ulva lactuca)

status: Public on Apr 13 2017

organism: Ulva lactuca


title: Illumina HiSeq 2000 (Acropora digitifera)

status: Public on Jan 19 2016

organism: Acropora digitifera


title: Agilent-042004 gallus_exp_microarray_SLagarrigue_8x60k_V2_july2012

status: Public on Jul 22 2016

city: Rennes

first: Colette

last: DESERT

address: 65 Rue de St Brieuc

country: France

institute: Agrocampus INRA UMR1348 PEGASE

organism: Gallus gallus

description:
Arrays of this design have barcodes that begin with 16042004 or 2542004.
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 FeatureNum 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: Sandrine

last: Lagarrigue


title: Agilent-034068 Arraystar Mouse LncRNA microarray V2.0 [feature number version]

status: Public on Dec 31 2014

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

organism: Mus musculus

manufacture_protocol: see website


title: Ion Torrent S5 (Homo sapiens)

status: Public on Aug 17 2017


title: Agilent-015421 Rhesus Macaque Gene Expression Microarray (Probe Name Version)

status: Public on Sep 12 2011

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
M. mulatta (Rhesus) Oligo Microarray 4x44K

Arrays of this design have barcodes that begin with 16015421 or 2515421.

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.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL9861

relation: Alternative to: GPL9861 (Feature Number Version)


title: Illumina Genome Analyzer II (Drosophila melanogaster)

status: Public on Aug 20 2009

organism: Drosophila melanogaster