title: Affymetrix HuGene-1_0-st-v1 [ORF]

status: Public on Aug 23 2023

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: see Affymetrix


title: NanoString nCounter Mouse Neuroinflammation Panel

status: Public on Feb 13 2023

city: Riverside

first: Djurdjica

last: Coss

state: CA

address: 900 University Ave

department: Biomedical Sciences

country: USA

institute: UC Riverside

organism: Mus musculus

technology: other


title: KARC Schizosaccharomyces pombe 5K Ver. E ORF array

status: Public on Mar 15 2006

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

organism: Schizosaccharomyces pombe

technology: spotted DNA/cDNA

description: The breakdown of 5184 spots is as follows; 4929 fission yeast genes (cdc2, nuc1, and nda3 are excluded) are spotted once on a slide, cdc2, nuc1, nda3, and GFP are spotted once for each block (16 in total). Representative values of r' for these 4 genes were average of their 16 spots. ID numbers from 5185 to 5188 are assigned to their representative values. 11 negative control spots are common to each block (A to P except for G block, 175 in total). In G block, one of 11 Negative controls spots is replaced with LEU2 (S.cerevisiae). The reaction mixture except primers was spotted at negative control spots. Only spotting buffer were spotted at 8 blank spots. Spots for the following 7 ORF, SPAC212.10, SPAC3G9.16c, SPBC19G7.12c, SPCC784.05c, SPCC1442.04c, SPAC8E11.04c, SPBC2A9.08c, are ignored in data processing (see details in http://www-karc.nict.go.jp/d332/CellMagic/index.html).

distribution: non-commercial

manufacturer: National Institute of Information and Communications Technology, and Japan Science and Technology Agency

first: Yuji

last: Chikashige

first: Chihiro

last: Tsutsumi

first: Tokuko

last: Haraguchi

first: Yasushi

last: Hiraoka

manufacture_protocol: Probe DNA used for the microarray was generated by PCR from the code region of each gene that has been described in annotated fission yeast genome sequences(Wood et al., 2002 Nature 415, 871-880). The continuous 300bp+/- 10bp exon sequence nearest to the 3'-end of the gene was selected as a probe. When the longest exon of the gene is shorter than 290bp, the longest exon was used as a probe. The primer used for PCR was designed by using the primer design supporting tool, Primer3(http:://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi). The length of each primer is 30+/-3bp. Tm of the primer is 60-70C. The forward primers are modified by the amino group at their 5' end. Wild type L972 strain's genome DNA was used as the temperate of the first rounds of PCR. For the second and later round of PCR, the PCR products of the first round of PCR were used as a temperate. GeneAmp PCR System9700(Applied Biosystemes) and z-Taq polymerase(Takara) were used for PCR. PCR was done as follows: 40 cycles, 95C for denature, 72C for extension, for annealing 54-63C according to the Tm value of primers.The PCR product was purified by using Multiscreen96(Millipore) or NucleoFast96(MACHEREY-NAGEL) and measured the density by using SpectraMax190(Molecular Devices). A part of the product was confirmed by agarose gel electrophoresis. The dried up probe DNA 4 microg is dissolved in 20 microl spotting buffer (150mM Na-phosphate buffer pH8.5). Probe DNA was stamped on Surmodics 3D-Link Slide by GTMASS STAMPER (Nippon Laser Electronics). 16 pins of GTMASS STAMPER stamp 324(18x18) times respectively on a slide to form 16 blocks (A to P) including 5184(16x18x18) spots in total. The diameter of each spot is about 150 microm, and the pitch is 190 microm. The stamped slides are incubated in a humidity chamber (about 75% in humidity) for 2days, then are soaked in a pre-warmed blocking buffer (50mM ethanolamine, 0.1M Tris-Cl pH9, 0.1% SDS) at 50C, for 15-30 minutes. The slides were rinsed twice with distilled water (DW), and soaked in a wash buffer (4xSSC, 0.1% SDS) at 50C, for 15-60 minutes. then, are rinsed twice with DW, and boiled in DW for 2 minutes. After rinsing twice in DW, the slides were dried up.


title: PromethION (Actinobacillus pleuropneumoniae)

status: Public on Jan 30 2023

last: GEO

organism: Actinobacillus pleuropneumoniae

technology: high-throughput sequencing

distribution: virtual


title: NanoString nCounter PanCancer Immune Profiling Panel

status: Public on Feb 01 2023

city: Boston

first: Sonu

last: Subudhi

state: MA

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

manufacture_protocol: see manufacturer's website


title: Qiagen Custom miScript miRNA PCR Arrays

status: Public on Jan 31 2023

city: Shenyang

first: Ming

last: He

state: Liaoning

address: No. 36 Sanhao Street

country: China

institute: Shengjing Hospital of China Medical University

technology: RT-PCR

description: qPCR assay


title: Illumina HiSeq 4000 (Pteronotus quadridens)

organism: Pteronotus quadridens


title: Illumina HiScanSQ (Porphyromonas gingivalis)

organism: Porphyromonas gingivalis


title: Agilent-086188 Agilent Human ceRNA Microarray 2019

status: Public on Feb 02 2023

city: Shanghai

first: Ping

last: Zheng

state: Shanghai

address: 490 South Chuanhuan Road

department: Neurosurgery

institute: Shanghai Pudong New area People's Hospital

distribution: commercial

manufacture_protocol: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. The probes detected with at least 75.0 percent in any group were chosen for further data analysis.


title: Illumina HiSeq 2500 (Digitalis lanata)

organism: Digitalis lanata


title: NanoString GeoMx DSP

status: Public on Mar 07 2023

city: Charlottesville

first: Ana Karina

last: de Olliiveirra

state: VA

address: 1340 Jefferson Park Avenue

department: Department of Pathology

institute: UVA

description: Spatial Proteomics - Barcode readout counts

manufacture_protocol: NanoString GeoMx DSP


title: Illumina HiSeq 4000 (Erophylla sezekorni)

organism: Erophylla sezekorni


title: Illumina EUChip60k SNP array

city: Guangzhou

first: Huixiao

last: Yang

state: Guangdong

address: No 233 1st Guangshan Road

institute: Guangdong Academy of Forestry

organism: Eucalyptus urophylla

technology: oligonucleotide beads

description: Detailed info on the SNP contained in this chip (genome location, target SNP, flanking sequence) in Silva-Junior et al. (2015).  See Table S3 Infinium SNP probe sequence, ADT score and genome coordinate of the 60 904 SNPs of the EUChip60k.

manufacture_protocol: see Illumina web site


title: Illumina HiSeq 2500 (Lathyrus sativus)

status: Public on Jan 29 2023

organism: Lathyrus sativus


title: PromethION (Escherichia coli)

organism: Escherichia coli


title: Illumina NextSeq 500 (Perkinsus marinus)

status: Public on Jan 28 2023

organism: Perkinsus marinus


title: Illumina NextSeq 500 (Haloferax mediterranei)

organism: Haloferax mediterranei


title: Agilent-078298 human ceRNA array [Probe Name Version]

city: Nanchang

first: xijuan

last: liu

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

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


title: Illumina NextSeq 500 (Sphaeroforma arctica)

organism: Sphaeroforma arctica


title: Illumina NextSeq 500 (Creolimax fragrantissima)

organism: Creolimax fragrantissima


title: NextSeq 2000 (Bacillus subtilis; Escherichia coli)

status: Public on Jan 26 2023

organism:
Escherichia coli
Bacillus subtilis


title: NextSeq 2000 (Clostridium perfringens)

organism: Clostridium perfringens


title: Illumina NovaSeq 6000 (Tomato curly stunt virus)

status: Public on Jan 25 2023

organism: Tomato curly stunt virus


title: Agilent-032812 Custom IMB/D. melanogaster array

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

organism: Drosophila melanogaster

description:
Drosophila Fly IMB
Arrays of this design have barcodes that begin with 16032812 or 2532812.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina HiSeq 3000 (Acinetobacter baumannii ATCC 17978)

status: Public on Jan 23 2023

organism: Acinetobacter baumannii ATCC 17978


title: Illumina NovaSeq 6000 (Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74)

status: Public on Jan 24 2023


title: Illumina HiSeq 2500 (Canis lupus)

status: Public on Jan 27 2023

organism: Canis lupus


title: Illumina NovaSeq 6000 (Brevibacillus brevis)

organism: Brevibacillus brevis


title: Duke/086684

status: Public on Jan 20 2023

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

organism: synthetic construct

manufacture_protocol: In situ oligosynthesized array with synthetic sequences.


title: Illumina HiSeq 4000 (Mus musculus; Rattus norvegicus)

status: Public on Jan 21 2023

organism:
Mus musculus
Rattus norvegicus


title: Illumina NextSeq 500 (Spirosoma montaniterrae)

organism: Spirosoma montaniterrae


title: Illumina NextSeq 500 (Dryas iulia)

organism: Dryas iulia


title: Illumina NovaSeq 6000 (Brassica rapa var. parachinensis)

organism: Brassica rapa var. parachinensis


title: Illumina NovaSeq 6000 (Americamysis bahia)

organism: Americamysis bahia


title: Duke/085400


title: Duke/085438


title: Duke/084702


title: Illumina HiSeq 4000 (Caecomyces churrovis; Fibrobacter succinogenes)

organism:
Fibrobacter succinogenes
Caecomyces churrovis


title: Illumina NextSeq 500 (Caecomyces churrovis; Fibrobacter succinogenes)


title: Illumina NextSeq 500 (Fibrobacter succinogenes)

organism: Fibrobacter succinogenes


title: Illumina HiSeq 4000 (Fibrobacter succinogenes)


title: Illumina NextSeq 500 (Anaeromyces robustus; Fibrobacter succinogenes)

organism:
Fibrobacter succinogenes
Anaeromyces robustus


title: Illumina HiSeq 4000 (Anaeromyces robustus; Fibrobacter succinogenes)


title: Illumina HiSeq 4000 (Geobacter metallireducens)

organism: Geobacter metallireducens


title: Illumina HiSeq 2000 (Xanthoceras sorbifolium)

organism: Xanthoceras sorbifolium


title: Illumina NextSeq 500 (Geobacter metallireducens)


title: HiSeq X Ten (Sebastes schlegelii)

status: Public on Jan 19 2023

organism: Sebastes schlegelii


title: Duke/086688


title: Illumina NovaSeq 6000 (Plasmodium yoelii yoelii 17XNL)

status: Public on Jan 18 2023

organism: Plasmodium yoelii yoelii 17XNL


title: Illumina NextSeq 500 (Geobacter sulfurreducens)

organism: Geobacter sulfurreducens


title: Illumina HiSeq 2000 (Nannochloropsis oceanica strain IMET1)

organism: Nannochloropsis oceanica strain IMET1


title: [Celegans] Affymetrix C. elegans Genome Array [CDF: Celegans_Ce_ENSG version 21]

city: Nicosia

first: Constantinos

last: Deltas

state: Aglantzia

address: Palaios dromos Lefkosias Lemesou No.215/6

department: Biology

country: Cyprus

institute: University of Cyprus

organism: Caenorhabditis elegans

description: This is identical to GPL200 but a custom CDF environment was used to extract data [Brainarray Version 21, Celegans_Ce_ENSG]. CDF can be downloaded from the Brainarray website: http://mbni.org/customcdf/21.0.0/ensg.download/Celegans_Ce_ENSG_21.0.0.zip

relation: Alternative to: GPL200 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Heterosigma akashiwo)

organism: Heterosigma akashiwo


title: Illumina NovaSeq 6000 (Citrus x paradisi)

organism: Citrus x paradisi


title: Illumina HiSeq 1500 (Drosophila biarmipes)

status: Public on Jan 12 2023

organism: Drosophila biarmipes


title: Illumina NextSeq 500 (Escherichia coli BL21(DE3))

organism: Escherichia coli BL21(DE3)


title: Illumina MiniSeq (Escherichia coli BL21(DE3))


title: Illumina NovaSeq 6000 (Sesamum indicum)

status: Public on Jan 17 2023

organism: Sesamum indicum


title: Illumina NextSeq 500 (Fukomys damarensis)

status: Public on Jan 16 2023

organism: Fukomys damarensis


title: HiSeq X Ten (Aedes albopictus)

status: Public on Jan 11 2023

organism: Aedes albopictus


title: Utz Lab CTD Array

city: Stanford

first: Allan

last: Feng

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

organism:
Escherichia coli
Triticum aestivum
Spodoptera frugiperda
Homo sapiens
Sus scrofa
Bos taurus
Capra hircus

technology: spotted peptide or protein

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: Illumina HiSeq 4000 (Coelomomyces lativittatus)

status: Public on Jan 05 2023

organism: Coelomomyces lativittatus


title: Illumina NextSeq 500 (Elaeis guineensis)

status: Public on Jan 10 2023

organism: Elaeis guineensis


title: NextSeq 2000 (Canis lupus familiaris)

organism: Canis lupus familiaris


title: Agilent-085630 Oebiotech Human Microarray V7 [probe version]

city: Zhengzhou

first: Yuan

last: Yuan

state: Henan

address: No. 3, Fukang Front Street, Erqi District, Zhengzhou, Henan Province

institute: The Fifth Affiliated Hospital of Zhengzhou University

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16085630 or 2585630.

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 (Aspergillus fumigatus)

organism: Aspergillus fumigatus


title: Agilent-086310 human CANCER_SNV_02 array

status: Public on Jan 09 2023

first: Trevor

last: Siggers

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

manufacture_protocol: see Agilent


title: Illumina NovaSeq 6000 (Purpureocillium lavendulum)

organism: Purpureocillium lavendulum


title: Illumina HiSeq 2500 (Bienertia sinuspersici)

status: Public on Jan 14 2023

organism: Bienertia sinuspersici


title: Agilent-086772 human CANCER_SNV_v3 array


title: Utz Lab ACA Array

organism:
Escherichia coli
Homo sapiens


title: Illumina HiSeq 4000 (Zymoseptoria tritici)

status: Public on Jan 04 2023

organism: Zymoseptoria tritici


title: Illumina HiSeq 3000 (Dunaliella tertiolecta)

organism: Dunaliella tertiolecta


title: Illumina NovaSeq 6000 (Mycobacterium tuberculosis variant bovis)


title: [GO_Screen] Affymetrix human GO_Screen Assay

status: Public on Jan 03 2023

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: ThermoFisher GO_Screen

manufacture_protocol: See manufacturer's website


title: Illumina NovaSeq 6000 (Mycobacteroides abscessus ATCC 19977)

organism: Mycobacteroides abscessus ATCC 19977


title: Illumina NovaSeq 6000 (Trichoderma reesei QM6a)

organism: Trichoderma reesei QM6a


title: Illumina HiSeq 3000 (Dunaliella salina)

organism: Dunaliella salina


title: Illumina NovaSeq 6000 (Synechococcus elongatus PCC 7942 = FACHB-805)


title: DNBSEQ-G400 (Picea abies)

organism: Picea abies


title: [Axiom_HGCoV2_1] Axiom Human Genotyping SARS-CoV-2 Research Array

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

manufacture_protocol: see web site


title: Agilent-028936 KARC-EX-2010-31 026058 [Feature Number version]

status: Public on Mar 04 2015

first: Atsushi

last: Matsuda

institute: National Institute of Information and Communications Technology

organism: Schizosaccharomyces pombe

description:
Arrays of this design have barcodes that begin with 16028936 or 2528936.

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: GPL15360 (Probe name version)


title: QIAGEN RT2 Profiler PCR Array Rabbit Wound Healing PANZ-121Z

status: Public on Jan 02 2023

city: CPH

first: Constance

middle: E

last: Grandjean

address: Blegdamsvej 3

department: Cluster for Molecular Imaging

country: Denmark

institute: University of Copenhagen

organism: Oryctolagus cuniculus

description: PCR assay


title: Illumina Infinium MethylationEPIC version 2

status: Public on Jan 15 2023

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.


title: KARC Schizosaccharomyces pombe 5K Ver. F ORF array

status: Public on Apr 01 2009

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

manufacturer: National Institute of Information and Communications Technology

first: Yuji

last: Chikashige

first: Chihiro

last: Tsutsumi

first: Tokuko

last: Haraguchi

first: Yasushi

last: Hiraoka

manufacture_protocol:
Probe DNA used for the microarray was generated by PCR from the code region of each gene that has been described in annotated fission yeast genome sequences(Wood et al., 2002 Nature 415, 871-880). The continuous 300bp+/- 10bp exon sequence nearest to the 3'-end of the gene was selected as a probe. When the longest exon of the gene is shorter than 290bp, the longest exon was used as a probe. The primer used for PCR was designed by using the primer design supporting tool, Primer3(http:://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi). The length of each primer is 30+/-3bp. Tm of the primer is 60-70°C. The forward primers are modified by the amino group at their 5' end. Wild type L972 strain's genome DNA was used as the temperate of the first rounds of PCR. For the second and later round of PCR, the PCR products of the first round of PCR were used as a temperate. GeneAmp PCR System9700(Applied Biosystemes) and z-Taq polymerase(Takara) were used for PCR. PCR was done as follows: 40 cycles, 95°C for denature, 72°C for extension, for annealing 54-63°C according to the Tm value of primers.
The PCR product was purified by using Multiscreen96(Millipore) or NucleoFast96(MACHEREY-NAGEL) and measured the density by using SpectraMax190(Molecular Devices). A part of the product was confirmed by agarose gel electrophoresis. The dried up probe DNA 4 micro g is dissolved in 20 microl spotting buffer (150mM Na-phosphate buffer pH8.5). Probe DNA was stamped on Surmodics 3D-Link Slide by GTMASS STAMPER (Nippon Laser Electronics). 16 pins of GTMASS STAMPER stamp 324(18x18) times respectively on a slide to form 16 blocks (A to P) including 5184(16x18x18) spots in total. The diameter of each spot is about 150 microm, and the pitch is 190microm. The stamped slides are incubated in a humidity chamber (about 75% in humidity) for 2days, then are soaked in a pre-warmed blocking buffer (50mM ethanolamine, 0.1M Tris-Cl pH9, 0.1% SDS) at 50°C, for 15-30 minutes. The slides were rinsed twice with distilled water (DW), and soaked in a wash buffer (4xSSC, 0.1% SDS) at 50°C, for 15-60 minutes. then, are rinsed twice with DW, and boiled in DW for 2 minutes. After rinsing twice in DW, the slides were dried up.


title: Agilent-086103 Carassius auratus (goldfish) array

status: Public on Jan 01 2023

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

organism: Carassius auratus


title: Illumina HiSeq 3000 (Bacteriophage sp.)

last: GEO

organism: Bacteriophage sp.


title: Agilent-038274 Schizosaccharomyces pombe KARC-EX-20120118 [Feature Number version]

status: Public on Oct 22 2015

city: Kobe

description:
Arrays of this design have barcodes that begin with 16038274 or 2538274.
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: KARC Schizosaccharomyces pombe 5K Ver. D2 ORF array

status: Public on Dec 01 2007


title: KARC Schizosaccharomyces pombe 5K Ver. E2 ORF array


title: ThermoFisher TaqMan™ OpenArray™ Human MicroRNA Panel, QuantStudio™ 12K Flex (Catalog number: 4470187)

status: Public on Apr 27 2022

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

country: Spain

institute: Institute of Biomedicine of Seville

description: Ref. 4470187, Life Technologies, Carlsbad, USA


title: Agilent-038274 Schizosaccharomyces pombe KARC-EX-20120118 [condensed version]

status: Public on Mar 31 2015

description:
Arrays of this design have barcodes that begin with 16038274 or 2538274.

This array includes 6767 probes. 56 probes represent two or more genes.
Perfect identical sequences of 27 probes are found in 2 or more genes. These 27 probes represent 71 genes in total. Details of these probes and the represented genes are included in the Platform data table and in the supplementary file 'GSE18374_dup27.txt'.
The other 29 probes, which have IDs such as 400xx_tel-XXX, come from chromosome end regions. The ends of the 1st and 2nd chromosomes have very similar sequences in 50 more kb. Thus, some sequences in the region are found 4 times. However, because there are some deletions or duplications, the sequences are not always duplicated 4 times. So, 9 out of 29 probes actually  represent only one gene, and the other 20 probes represent 2 or more genes. These details are in the supplementary file 'GSE18374_tel29.txt'.
Correction information for cross-hybridized probes are in the supplementary files 'GPL18374_Supplemental_procedure.txt' and 'GPL18374_Correction-probes.txt'.


title: KARC Schizosaccharomyces pombe 5K Ver. D ORF array

status: Public on Mar 20 2006

description: The breakdown of 5184 spots is as follows; 4929 fission yeast genes (cdc2, nuc1, and nda3 are excluded) are spotted once on a slide, cdc2, nuc1, nda3, and GFP are spotted once for each block (16 in total). Representative values of r' for these 4 genes were average of their 16 spots. ID numbers from 5185 to 5188 are assigned to their representative values. 11 negative control spots are common to each block (A to P except, 176 in total). The reaction mixture except primers was spotted at negative control spots. Only spotting buffer were spotted at 8 blank spots. Spots for the following 7 ORF, SPAC212.10, SPAC3G9.16c, SPBC19G7.12c, SPCC784.05c, SPCC1442.04c, SPAC8E11.04c, SPBC2A9.08c, are ignored in data processing (see details in http://www-karc.nict.go.jp/d332/CellMagic/index.html).

manufacture_protocol:
Probe DNA used for the microarray was generated by PCR from the code region of each gene that has been described in annotated fission yeast genome sequences(Wood et al., 2002 Nature 415, 871-880). The continuous 300bp+/- 10bp exon sequence nearest to the 3'-end of the gene was selected as a probe. When the longest exon of the gene is shorter than 290bp, the longest exon was used as a probe. The primer used for PCR was designed by using the primer design supporting tool, Primer3(http:://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi). The length of each primer is 30+/-3bp. Tm of the primer is 60-70C. The forward primers are modified by the amino group at their 5' end. Wild type L972 strain's genome DNA was used as the temperate of the first rounds of PCR. For the second and later round of PCR, the PCR products of the first round of PCR were used as a temperate. GeneAmp PCR System9700(Applied Biosystemes) and z-Taq polymerase(Takara) were used for PCR. PCR was done as follows: 40 cycles, 95C for denature, 72C for extension, for annealing 54-63C according to the Tm value of primers.
The PCR product was purified by using Multiscreen96(Millipore) or NucleoFast96(MACHEREY-NAGEL) and measured the density by using SpectraMax190(Molecular Devices). A part of the product was confirmed by agarose gel electrophoresis. The dried up probe DNA 4 micro g is dissolved in 20 microl spotting buffer (150mM Na-phosphate buffer pH8.5). Probe DNA was stamped on Surmodics 3D-Link Slide by GTMASS STAMPER (Nippon Laser Electronics). 16 pins of GTMASS STAMPER stamp 324(18x18) times respectively on a slide to form 16 blocks (A to P) including 5184(16x18x18) spots in total. The diameter of each spot is about 150 microm, and the pitch is 190microm. The stamped slides are incubated in a humidity chamber (about 75% in humidity) for 2days, then are soaked in a pre-warmed blocking buffer (50mM ethanolamine, 0.1M Tris-Cl pH9, 0.1% SDS) at 50C, for 15-30 minutes. The slides were rinsed twice with distilled water (DW), and soaked in a wash buffer (4xSSC, 0.1% SDS) at 50C, for 15-60 minutes. then, are rinsed twice with DW, and boiled in DW for 2 minutes. After rinsing twice in DW, the slides were dried up.


title: KARC Schizosaccharomyces pombe CEN array

description: The 534 spots included: 514 spots which correspond to the sense or antisense strands of 257 sequences (ura4, GFP and 255 sequences from cen regions), and 20 negative control spots. ID number 50 and 306 are assigned to the #50 probes that were not included in the array (see the Manufacture Protocol).

first: Kasumi

last: Okamasa

manufacture_protocol:
255 probe sequences from centromere regions were generated by PCR. 173 of these sequences occurred between lys1 to the right edge of cntI. 56 sequences were from cen2, and the remaining 26 sequences from cen3. Probes for cen2 and cen3 were selected only from specific regions unique to each centromere. #50 probes of cen1 were not included in the array because they were not amplified by PCR. To make specific probes for each strand of the sequence, two primer sets were prepared for each sequence. In one set, the 5' end of the forward primer was modified with an amino group. In the other set, the 5' end of the reverse primer was modified with an amino group. A GeneAmp PCR System 9700 (Applied Biosystems) and z-Taq polymerase (TAKARA) were used for PCR. PCR conditions were as follows: 40 cycles of denaturation at 95°C, extension at 72°C, and annealing, depending on the Tm values of the primers, at 54-63°C. The PCR products were purified by using Multiscreen96 (Millipore) or NucleoFast96 (MACHEREY-NAGEL) kits and their concentrations were measured using a SpectraMax190 (Molecular Devices).
For each probe, 4µg of probe DNA was dissolved in 20µl spotting buffer (150mM Na-phosphate buffer pH8.5).These probes were spotted on a Surmodics 3D-Link Slide by a PixSys4500 (Genomic Solutions) to produce the centromere array. Spotting was carried out by the NippnTecnoCrasta e-Array system. 534 spots were applied to each cen array. The diameter of each spot was 380µm and the pitch 920µm. To covalently bind probe DNA to the glass slide, a blocking procedure was carried out as follows: the stamped slides were incubated in a humidity chamber (~75% humidity) for 2 days, and then were soaked in a pre-warmed blocking buffer (50mM ethanolamine, 0.1M Tris-Cl pH9, 0.1% SDS) at 50°C for 15-30 minutes. The slides were rinsed twice with distilled water (DW), soaked in a wash buffer (4xSSC, 0.1% SDS) at 50°C for 15-60 minutes, and again rinsed twice with DW. To remove the unmodified anti sense strand of the probe DNA, the slides were boiled in DW for 2 min. After rinsing twice in DW, the slides were dried.


title: Agilent-028936 KARC-EX-2010-31 026058 [ProbeName version]

status: Public on Jun 26 2012

relation: Alternative to: GPL19837 (Feature Number version)


title: [RaGene-1_0-st] Affymetrix Rat Gene 1.0 ST Array [transcript (gene) version]

status: Public on Dec 05 2007

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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

#%create_date=Wed Mar 11 16:20:04 2009 PDT
#%chip_type=RaGene-1_0-st-v1
#%lib_set_name=RaGene-1_0-st
#%lib_set_version=v1
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-ncbi=HGSC v3.4
#%genome-version-create_date=2004-11
#%netaffx-annotation-date=2009-03-16
#%netaffx-annotation-netaffx-build=28

relation: Alternative to: GPL17378 (Alternative CDF [RaGene10stv1_Rn_ENTREZG])

relation: Alternative to: GPL17896 (Alternative CDF [RaGene10stv1_Rn_ENTREZG_V14])

relation: Alternative to: GPL32992 (Alternative CDF [RaGene10stv1_Rn_ENTREZG_V20])

manufacture_protocol: See manufacturer's web site