title: SABiosciences/Qiagen Human Cellular Senescence RT² Profiler PCR Array

status: Public on Feb 29 2016

city: Vilnius

first: Gabrielis

last: Kundrotas

address: Santariškių str. 1

country: Lithuania

institute: National Cancer Institute

organism: Homo sapiens

technology: RT-PCR

description: PCR array profiles the expression of 84 key genes involved in the initiation and progression of the biological process causing cells to lose the ability to divide

distribution: virtual

manufacture_protocol: see manufacturer's website


title: SABiosciences/Qiagen Human miRNome miScript miRNA PCR Array

description: PCR array profiles the expression of the most abundantly expressed and best characterized miRNA sequences in the human miRNA genome (miRNome)


title: JCVI PFGRC Streptococcus gordonii 16K v1 array designed primarily based on strain Challis (Feature ID)

status: Public on Aug 20 2015

city: Buffalo

first: M

middle: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Periodontics and Endodontics

country: USA

institute: University at Buffalo

organism: Streptococcus gordonii

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: SG, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: SABiosciences/Qiagen Human Mesenchymal Stem Cell RT² Profiler PCR Array

description: PCR array profiles the expression of 84 key genes involved in maintaining pluripotency and self-renewal status


title: Affymetrix Rice Genome Array (custom CDF; RAGP7)

status: Public on May 31 2015

city: Potsdam

first: Xia

last: Li

address: Am Mühlenberg 1

country: Germany

institute: Max-Planck-Institute of Molecular Plant Physiology

organism: Oryza sativa

technology: in situ oligonucleotide

description:
The custom CDF file containing all selected probes was created using ArrayInitiative.
Gene-level synonymous probesets were grouped according to corresponding gene ID, based on the Affymetrix Rice Annotation File (Release 29, 07/01/09).
Gene locus IDs were obtained from the MSU Rice Genome Annotation Project gene set (release RAGP 7; http://rice.plantbiology.msu.edu/index.shtml) and the Rice Annotation Project Database (RAP-DB), gene function annotation was according to RGAP 7.

relation: Alternative to: GPL2025 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: NCSU C. kronotskyensis 3K v1.0

status: Public on Jul 31 2015

city: Raleigh

first: Jeffrey

last: Zurawski

state: NC

address: 840 Main Campus Drive Room 3309

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

organism: Caldicellulosiruptor kronotskyensis

manufacture_protocol: A DNA microarray was designed and constructed based on 2583 protein-coding sequences in the C. kronotskyensis genome obtained from the Department of Energy's Joint Genomics Institute (https://img.jgi.doe.gov). OligoArray 2.1 (Rouillard, 2003) was used to generate one 30 to 60-mer oligonucleotide probe sequence for each open reading frame. The probes were synthesized (Integrated DNA Technologies, IA), re-suspended in 50% DMSO, and printed onto Ultragap microarray slides (Corning, NY) using a QArrayMini arrayer (Genetix, UK). Each probe was spotted five times onto each array to fortify statistical analysis.


title: DSM PENa520255F Penicillium chrysogenum 14k v1.0

status: Public on Aug 28 2008

city: Delft

first: Marco

middle: Alexander

last: van den Berg

address: PO Box 425

country: Netherlands

institute: DSM Anti Infectives

organism: Penicillium chrysogenum

description: Penicillium chrysogenum strain Wisconsin 54-1255

distribution: custom-commercial

middle: A

first: Noël

middle: N

last: van Peij

first: Johannes

last: Roubos

first: Wilbert

middle: H

last: Heijne

first: Roel

last: Bovenberg

manufacture_protocol:
Affymetrix Custom GeneChip program, 49-7875 format, 11μm features. 11 probe pairs per set. The CDF file is linked below as a supplementary file.
GeneChip design Based on the genome sequence of Wisconsin54-1255, a proprietary GeneChip®, DSM_PENa520255F, was designed for DSM according to the Custom GeneChip® program by Affymetrix (Affymetrix, Inc., Santa Clara, CA). The chips of the 49-7875 format contain 11μm features. There are 11 pairs of 25-oligonucelotides in each probe set representing each of the approximately 13670 annotated ORFs and supplemented with genetic elements and a selection of large intergenic sequences of P. chrysogenum. The probe sequences were designed based on the region in the (predicted) coding sequence stretching from 650 to 4 nt, from the 3’ end. Typical Affymetrix control probe sets were included (B. subtilis, E. coli, Bacteriophage P1 and A. thalinana spike controls). For several known P. chrysogenum genes, separate 3’ end, middle and 5’ end probe sets were designed that allow monitoring the efficiency of the in vitro transcription reaction. In addition, 1551 probe sets were included to search for the presence of yet unpredicted ORFs within large sequences (>2500nt) between two predicted ORFs or genetic elements. For this, the ‘intergenic’ regions were split up in 800 nt fragments (skipping 300nt from each end) and probe sets were designed for both strands (coding and reverse complement) for the sequences stretching from 300-1100 (gn3, 494 sets); 1900-2700 (gn5, 177 sets) ; 3500-4300 (gn7, 44 sets); 5100-5900(gn9, 5 sets); 6700-7500 (gn11, 5 sets); 8300-9200 (gn13, 2 sets) and 10000-10800 (gn15, 2 sets) until the 300nt from the 5’end of the region. Intergenic regions on the border of two contigs were represented by two probe sets marked with A and B (i.e.. gn3A, gn3B and gn5A, gn5B).


title: Agilent-018897 Unrestricted Human Genome CNV Microarray 244K (1 of 2)

status: Public on May 29 2015

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Unrestricted Human Genome CNV Microarray, 1x244K (1 of 2)

Arrays of this design have barcodes that begin with 16018897 or 2518897.

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: Agilent-034168 Shirasu-JK002-13May2011 [Probe Name Version]

city: Yokohama

first: Juliane

middle: Karine

last: Ishida

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

organism: Phtheirospermum japonicum

description: The sequences used to design the probes for this array came from an RNA-Seq study of Phtheirospermum japonicum. The sample used for RNA-Seq is accessioned in NCBI's BioSample database: SAMN03271814.


title: Illumina HiSeq 2000 (Selaginella kraussiana)

last: GEO

organism: Selaginella kraussiana

technology: high-throughput sequencing


title: Agilent-018898 Unrestricted Human Genome CNV Microarray 244K (2 of 2)

description:
Unrestricted Human Genome CNV Microarray, 1x244K (2 of 2)

Arrays of this design have barcodes that begin with 16018898 or 2518898.

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 MiSeq (Streptomyces coelicolor)

status: Public on May 28 2015

organism: Streptomyces coelicolor


title: NCSU C. bescii 3K v1.0

organism: Caldicellulosiruptor bescii

manufacture_protocol: A DNA microarray was designed and constructed based on 2674 protein-coding sequences in the C. bescii genome obtained from the Department of Energy's Joint Genomics Institute (https://img.jgi.doe.gov). OligoArray 2.1 (Rouillard, 2003) was used to generate one 30 to 60-mer oligonucleotide probe sequence for each open reading frame. The probes were synthesized (Integrated DNA Technologies, IA), re-suspended in 50% DMSO, and printed onto Ultragap microarray slides (Corning, NY) using a QArrayMini arrayer (Genetix, UK). Each probe was spotted five times onto each array to fortify statistical analysis.


title: Illumina HiSeq 2500 (Triticum turgidum subsp. durum)

organism: Triticum turgidum subsp. durum


title: Illumina HiSeq 2500 (Rana catesbeiana)

status: Public on May 26 2015

organism: Aquarana catesbeiana


title: Agilent-028279 SurePrint G3 Rat GE Microarray 8x60K [Gene symbol + Agilent Probe ID]

city: Chicago

first: J. Ruth

last: Wu-Wong

state: IL

address: 2201 W. Campbell Park Dr., Suite 13

institute: Vidasym

organism: Rattus norvegicus

description:
This platform has been organized with a mixture of the unique gene symbols, GenBank Accessions and Agilent Probe IDs in the 'ID' column.
This array platform includes the ERCC probe sequences. Identical feature numbers and probe sequences as GPL13521.

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


title: Illumina NextSeq 500 (Drosophila virilis)

organism: Drosophila virilis


title: Illumina NextSeq 500 (Drosophila busckii)

organism: Drosophila busckii


title: 101230_VR_Cdiff_strains_expr

status: Public on May 27 2015

city: Iowa City

first: Craig

middle: D.

last: Ellermeier

state: IA

address: 51 Newton Rd 3-630 BSB

department: Microbiology

institute: University of Iowa

organism: Clostridioides difficile 630

description:
Prokaryote Expression 12x135K custom array delivery; design name, 101230_VR_Cdiff_strains_ex- pr_HX12; design no. 546991). Each of the 12 subarrays included 18 probes (60 oligomers each) homologous to 3,786 of the 3,787 open reading frames of the C. difficile 630 genome as well as negative hybridization controls. TheNimbleGen design name 101230_VR_Cdiff_strains_expr.ndf, NimbleGen RNG# 560976  A 12x135K expression design for 4,302 genes from Clostridium difficile CD630 and Clostridium difficile R20291.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

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


title: Agilent-055694 Bacillus Calmette Guerin 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

country: China

institute: MSP

organism: Mycobacterium tuberculosis variant bovis BCG

description: Bacillus Calmette Guerin (BCG)


title: Agilent-021365 SurePrint G3 Human CNV Microarray 2x400K (Probe Name version)

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
Agilent's SurePrint G3 Human CNV Microarray, 2x400K

Arrays of this design have barcodes that begin with 16021365 or 2521365.

Data table annotations based on build hg18:NCBI36:Mar2006.

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.

distribution: commercial


title: Illumina HiSeq 2000 (Coxsackievirus B2 (strain Ohio-1); Homo sapiens)

organism:
Homo sapiens
Coxsackievirus B2 (strain Ohio-1)


title: Illumina HiSeq 2000 (Pseudomonas protegens)

status: Public on May 22 2015

organism: Pseudomonas protegens


title: Illumina HiSeq 2000 (Arthrobotrys cylindrospora)

status: Public on May 21 2015

organism: Dactylella cylindrospora


title: Ion Torrent Proton (Citrus unshiu)

status: Public on May 23 2015

organism: Citrus unshiu


title: GeoChip 5.0 [Central South University]

city: Changsha

first: Jing

last: Cong

address: Yuelushan

institute: Central South University

organism:
Bacteria
Archaea
Eukaryota


title: Illumina HiSeq 2000 (Drechslerella brochopaga)

organism: Orbilia brochopaga


title: Illumina HiSeq 2000 (Arthrobotrys oligospora)

organism: Orbilia oligospora


title: Human OncoBAC CGH

status: Public on May 20 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

organism: Homo sapiens

technology: spotted DNA/cDNA

manufacture_protocol: OncoBAC arrays were comprised of 960 P1, PAC, or BAC clones. About three-quarters of the clones on the OncoBAC arrays contained genes and STSs implicated in cancer development or progression. All clones were printed in quadruplicate.


title: Agilent-036832 Ferret_44K_v3

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

organism: Mustela putorius furo

description:
Arrays of this design have barcodes that begin with 16036832 or 2536832.

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: Human Scanning CGH

manufacture_protocol: Scanning arrays were comprised of 2464 BACs selected at approximately megabase intervals along the genome as described previously (Hodgson et al., 2001 and Snijders et al., 2001).


title: Illumina HiSeq 2000 (Citrullus lanatus)

organism: Citrullus lanatus


title: Illumina HiSeq 2000 (Dendroctonus ponderosae)

status: Public on May 19 2015

organism: Dendroctonus ponderosae


title: Illumina Genome Analyzer (Dendroctonus ponderosae)


title: Illumina chicken 60k SNP chip

city: Harbin

first: Hui

last: Zhang

state: Heilongjiang

address: Mucai street No. 59

department: College of Animal Science and Technology

institute: Northeast Agricultural University

organism: Gallus gallus

technology: oligonucleotide beads

manufacture_protocol: see Illumina web site


title: Illumina HiSeq 2500 (Escherichia coli HS)

organism: Escherichia coli HS


title: Illumina NextSeq 500 (Drosophila willistoni)

organism: Drosophila willistoni


title: Illumina HiSeq 2500 (Escherichia coli LF82)

organism: Escherichia coli LF82


title: NanoString nCounter miRNA Human v2.1

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

technology: other

description: Contributor: The Australian Ovarian Cancer Study Group

first: Ann

first: Elizabeth

middle: L

last: Christie

first: Dariush

last: Etemadmoghadam

first: Dale

middle: W

last: Garsed

first: Joshy

last: George

first: Sian

last: Fereday

first: Katia

last: Nones

first: Prue

last: Cowin

first: Kathryn

last: Alsop

first: Peter

middle: J

last: Bailey

first: Karin

middle: S

last: Kassahn

first: Felicity

last: Newell

first: Michael

middle: C

last: Quinn

first: Stephen

last: Kazakoff

first: Kelly

last: Quek

first: Charlotte

last: Wilhelm-Benartzi

first: Ed

last: Curry

first: Huei

last: San

first: San

last: Leong

first: Anne

last: Hamilton

first: Linda

last: Mileshkin

first: George

last: Au-Yeung

first: Catherine

last: Kennedy

first: Jillian

last: Hung

first: Yoke

middle: E

last: Chiew

first: Paul

last: Harnett

last: Friedlander

first: Jan

last: Pyman

last: Cordner

first: Patricia

last: O'Brien

first: Jodie

last: Leditschke

first: Greg

last: Young

first: Kate

last: Strachan

last: Waring

first: Walid

last: Azar

first: Chris

last: Mitchell

first: Nadia

last: Traficante

first: Joy

last: Hendley

first: Heather

last: Thorne

first: Mark

last: Shackleton

first: David


title: Illumina HiSeq 2500 (Ocimum americanum)

status: Public on May 18 2015

last: GEO

organism: Ocimum americanum


title: [HG-U133A] Affymetrix Human Genome U133A Array Custom Brainarray v15 [HGU133A_Hs_ENTREZG_15.0.0]

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Identical to GPL96 but used a custom CDF

manufacture_protocol: see the Affymetrix website


title: Agilent-01735 Custom Medaka 4x44K

status: Public on May 16 2015

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

organism: Oryzias latipes

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


title: Illumina HiSeq 2000 (Arthrobotrys entomopaga)

organism: Arthrobotrys entomopaga


title: Illumina HiSeq 2500 (Arabidopsis lyrata subsp. lyrata)

organism: Arabidopsis lyrata subsp. lyrata


title: Illumina MiSeq (Arabidopsis lyrata)

organism: Arabidopsis lyrata


title: Agilent-036227 Schizosaccharomyces pombe sp40c [ProbeName version]

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

organism: Schizosaccharomyces pombe

description:
Tm optimized 75C

Arrays of this design have barcodes that begin with 16036227 or 2536227.

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

The ID column represents the Agilent Probe Name.

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

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


title: Illumina HiSeq 2500 (Pantoea stewartii subsp. stewartii)

organism: Pantoea stewartii subsp. stewartii


title: PacBio RS II (Drosophila melanogaster)

status: Public on May 13 2015

organism: Drosophila melanogaster


title: PacBio RS II (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: Illumina Genome Analyzer IIx (Bradyrhizobium diazoefficiens USDA 110)

organism: Bradyrhizobium diazoefficiens USDA 110


title: Illumina NextSeq 500 (Mus musculus x Mus spretus)

organism: Mus musculus x Mus spretus


title: Illumina HiSeq 2000 (Peptoclostridium difficile R20291)

organism: Clostridioides difficile R20291


title: Agilent-019052 Homo sapiens 45k [Feature Number Version]

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

organism: Homo sapiens


title: Illumina MiSeq (Ovis aries)

status: Public on May 12 2015

organism: Ovis aries


title: Plants miRNA Array miRPlants_19_NJAU_121101a

status: Public on May 14 2015

city: Nanjing

first: Yue

last: Zhang

state: Jiangsu

address: Weigang No.1

department: Tea Science Research Institute

institute: Nanjing Agricultural University

organism: Embryophyta

description: The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [alternative CDF: Brainarray MoGene10stv1_Mm_REFSEQ_14.1.0]

status: Public on May 15 2015

first: GEO

last: admin

organism: Mus musculus

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
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/refseq.asp

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Agilent-067877 Homo sapiens hg19 Genocheck_CH3 G4820A

city: Ansan

first: jiyoung

last: hong

address: Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu

institute: hanyang university

description:
Arrays of this design have barcodes that begin with 16067877 or 2567877

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: GeoChip 4.6

city: Beijing

first: Mengjing

last: Xia

address: No.5 Yiheyuan Road

institute: Peking University

organism: Bacteria


title: Phanerochaete chrysosporium RP-78 microarrays (condensed array of GPL8022)

city: Vancouver

first: Shawn

last: Mansfield

state: BC

address: 2424 Main Mall

department: Department of Wood Science

country: Canada

institute: University of British Columbia

organism: Phanerochaete chrysosporium RP-78

description: The .ndf file is linked below as a supplementary file.

first: Dan

last: Cullen

manufacture_protocol: Proprietary maskless array in situ oligonucleotide synthesis. See http://www.nimblegen.com/


title: Agilent custom 1*1M chicken CGH array

city: Shenzhen

first: Guoqiang

last: Yi

state: Guangdong

address: No 7,Pengfei Road,Dapeng District,Shenzhen

institute: Agricultural Genome Institute at Shenzhen

organism: Gallus gallus


title: NimbleGen custom 3*1.4M chicken CGH array

description:
galGal4
A NimbleGen custom-designed 3*1.4M array based on galGal4 2011 build used in our experiment, which contained a total of 1425178 50-75mer probes with a mean and median interval of 734bp and 700bp.
120717_GalGal4_JH_CGH.ndf
120717_GalGal4_JH_CGH.pos

manufacture_protocol: NimbleGen


title: PacBio RS II (Nannochloropsis oceanica)

organism: Nannochloropsis oceanica


title: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MC4100)

status: Public on May 11 2015


title: Illumina HiSeq 2000 (Spalax carmeli)

organism: Spalax carmeli


title: Agilent-043965 custom human array oelinc_xw

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

description: Agilent-043965 oelinc_xw 042850


title: Illumina HiSeq 2000 (Acidovorax avenae subsp. avenae)

organism: Paracidovorax avenae


title: PacBio RS (Auricularia delicata)

organism: Auricularia delicata


title: PacBio RS II (Chlamydomonas reinhardtii)

organism: Chlamydomonas reinhardtii


title: PacBio RS II (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Illumina MiSeq (Plasmodium falciparum K1)

organism: Plasmodium falciparum K1


title: Illumina NextSeq 500 (Tribolium castaneum)

organism: Tribolium castaneum


title: Illumina HiSeq 2000 (Branchiostoma lanceolatum)

organism: Branchiostoma lanceolatum


title: Illumina NextSeq 500 (Nicrophorus vespilloides)

organism: Nicrophorus vespilloides


title: Mesorhizobium array [MrNa1]

status: Public on May 08 2015

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

organism: Mesorhizobium sp. N33

description:
Spotted PCR amplified from cloned genomic DNA digests. Each array has 48 blocks. Each block has 17 rows and 16 columns. Arrays were printed using the BioRobotics MicroGrid Compact spotter using Microsoft 10K split pins. Features vary from 70-110μm in diameter.

Please note that only a selection of clones have been sequenced and their sequences are provided in the 'platform_sequences.txt'.  The sequences are not of the entire clone (from one or both ends using SL1/SR2 primer). The sequences were assembled together to form contigs and to discover which clones were overlapping genomic sequences.

manufacturer: Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Ottawa, Ontario, Canada

manufacture_protocol: Arctic strain N33 cells were grown in 100 ml of YMB media with constant shaking (150 rpm) at room temperature (~21°C) to mid-log phase (OD600= 0.4-0.6) and cells were precipitated and washed in TES buffer (Gray et al., 1990) to eliminate extra-cellular polysaccharides ,by centrifugation (10,000g) at 4°C. Whole genomic DNA isolation was performed as described by Laberge et al., (1989) and stored at -20°C. DNA quality was verified using a NanoDrop 1000 spectrophotometer and by agarose gel (1%) electrophoresis. Two μg of DNA was mechanically sheared (Burger et al., 2007) using a nebulizer (Unomedical INC, McAllen, Texas USA, Ref #950-E) under nitrogen pressure of 20 psi for 3 minutes. DNA fragments ranging from 0.3-2 kb were subsequently blunt-ended using T4 DNA polymerase and Klenow DNA polymerase (Lucigen, Mississauga, Ontario). Blunt-ended DNA fragments (300 ng) were ligated to 50 ng/μl of blunt-ended pSMART-HC Kan vector (Lucigen,) and transformed into electro-competent E. coli DH5α cells (BIO-RAD). Plasmid inserts were amplified by standard PCR from 5760 clones (Biometra thermocycler) using the universal forward (SL1=5'-CAGTCCAGTTACGCTGGAGTC-3') and reverse primers (SR2=5'-GGTCAGGTATGATTTAAATGGTCAGT-3') complementary to vector sequences flanking the DNA inserts. Clones were digested with EcoRI (Boehringer Mannheim, Laval, Quebec, Canada) and fragment size and purity were evaluated by agarose gel electrophoresis. Some inserts were sequenced (Sanger et al., 1977) to verify that they were bona fide Rhizobium sequences by homology with the database GenBank. All recombinant E. coli clones were stored in glycerol at -85°C. Recombinant plasmid and PCR amplicons were stored at -20°C. PCR reactions from the Mesorhizobium strain N33 library were purified using the QIAquick 96 PCR Purification Kit (Qiagen, Cat. #28183) and transferred into the 384 master plate format using a Multiprobe II EX Robotic Liquid Handling System (Perkin Elmer, Shelton, CT). Plates were then dried without heat in a DNA 120 Speed Vac (Savant Instruments Inc., Holbrook, NY). Dried samples were resuspended in 10μl of 3XSSC and stored at -80°C. A total of 13,056 features, consisting of duplicate spots for each clone and 32 spike-in and negative controls for each block were arranged and printed on Corning GAPS II coated slides (Cat. # 40003), as per Corning instructions (www.corning.com/lifesciences). Arrays were printed using the BioRobotics MicroGrid Compact spotter (Digilab Inc, Holliston, MA). The arrays were snap-dried and DNA UV cross-linked to the slides using a CL-1000 ultraviolet cross linker (UPV, Upland, CA) for a total of 300 mJ.


title: Agilent-019760 custom human expression 244K microarray

first: Mervi

last: Heiskanen

organism: Homo sapiens


title: Exiqon miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno (miRBase v18.0)

status: Public on May 09 2015

first: Yan

last: Wang

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University


title: Agilent-042661 Aggregatibacter_Louisville [Probe Name version]

city: Louisville

first: Whitney

middle: Ann

last: Weigel

state: Kentucky

address: 501 S Preston St

department: OIID

institute: University of Louisville

organism: Aggregatibacter actinomycetemcomitans

description:
Louisville design

Arrays of this design have barcodes that begin with 16042661 or 2542661.

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.

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-034939 Bacillus_cereus_ATCC14579 [Feature Number Version]

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

institute: Tokyo University of Agriculture

organism: Bacillus cereus

description:
Arrays of this design have barcodes that begin with 16034939 or 2534939.

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: GPL20186 (Probe Name Version)


title: Agilent-034939 Bacillus_cereus_ATCC14579 [Probe Name Version]

relation: Alternative to: GPL20185 (Feature Number Version)


title: Agilent/IATS Sparus aurata oligonucleotide microarray 022077

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

organism: Sparus aurata

first: Jaume

last: Pérez-Sánchez

manufacture_protocol:
See manufacturer's web site at http://www.agilent.com/
AMADID: 022077


title: Illumina HiSeq 2000 (Histoplasma capsulatum)

last: GEO

organism: Histoplasma capsulatum


title: Illumina HiSeq 2000 (Blastomyces dermatitidis ATCC 26199)

organism: Blastomyces dermatitidis ATCC 26199


title: Luminex IMAP/Golub laboratory bead based miRNA platform 0.582K

city: Toronto

first: John

last: Dick

address: 101 College St. Toronto

institute: Ontario Cancer Institute

manufacture_protocol: See manufacturer's website


title: FGCVR_Arabidopsis_28K_v2.0

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

organism: Arabidopsis thaliana

manufacture_protocol: design on TAIR9 dataset, probe length =35-40mer, Combimatrix B3 Synthesizer, standard combimatrix synthesis protocol


title: Agilent-018073 Custom Brassica 60-mer two-color microarray [Probe Name version]

city: Bethesda

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Brassica

manufacture_protocol:
The assembled Brassica sequences (94,558 instances including those represented in both orientations) were submitted to Agilent Technologies’ eArray web portal for gene expression probe design. Probes with a base composition score greater than or equal to 3 were omitted from the final design; resulting in a total of 91,854 unique probes (including 6,989 derived from oppositely oriented pairs of sequences) that were included in the microarray design, of which 10,466 were predicted to have cross-hybridization potential.
11,893 probes were randomly selected to be represented in duplicate in the final design, which also included Agilent Technologies’ standard panel of quality control and spike-in probes.
Microarrays were manufactured using Agilent Technologies’ SurePrint Technology in the 2x104k format (two arrays containing ~104,000 probes on a single 1” x 3” glass slide).


title: Illumina HiSeq 2000 (Toxocara canis)

organism: Toxocara canis


title: Agilent-021086 Human CGH Whole Genome Microarray

status: Public on May 07 2015

city: Rockville

address: 9609 Medical Center Drive, 1W378

institute: NCI

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


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: GATExplorer_Ensembl v57]

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
The probes were mapped to GENE LOCi by the 'HuexonSpecificGeneProbes.tsv.gz' CDF built by GATExplorer

The 'transcripts-human-annotation.R.gz' annotation file (http://bioinfow.dep.usal.es/xgate/downloads_v57/transcripts-human-annotation.R.gz) is available at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=annotationfiles

relation: Alternative to: GPL5175 (Alternative CDF [official])

manufacture_protocol: see manufacturer's protocol


title: NimbleGen Rat RefSeq Promoter 720k array [090618_RN34_Refseq_Prom_ChIP]

city: Uppsala

first: Marcin

last: Kruczyk

address: Husargatan 3

country: Sweden

institute: Uppsala University

organism: Rattus norvegicus

description: DESIGN_NAME: 090618_RN34_Refseq_Prom_ChIP

manufacture_protocol: see NimbleGen website


title: Illumina HiSeq 2000 (Creolimax fragrantissima)

status: Public on May 06 2015

organism: Creolimax fragrantissima


title: Custom cDNA microarray representing 8,102 human genes

manufacture_protocol:
The 8102 human cDNA genes/clones used in this study were obtained from Research Genetics (Huntsville AB, USA) and were chosen from a set of 15,000 cDNA clones that corresponded to the Research Genetics Human Gene Filters sets GF200-202 (http://www.resgen.com/). This set of genes contained some redundancy (approximately 300 genes were printed more than once on each array) and contained approximately 4000 named genes, 2000 genes with homology to named genes in other species, and approximately 2000 ESTs of unknown function. In addition to these sequence verified clones, a small set (396) of clones whose sequence had not been verified were also included; all of these clones were excluded from all analyses presented in the figures. All of the non-sequence verified clones are identified in the primary data tables by the prefix SID (Stanford Identifier).
Detailed protocols are available at http://cmgm.stanford.edu/pbrown/array.html and http://cmgm.stanford.edu/pbrown/mguide/index.html


title: Agilent-021827 Human miRNA Microarray (V3) [miRNA_105_Jan09]

city: Lausanne

first: Fabian

last: Junker

state: VD

address: EPFL SV ISREC - UPRAD, SV2533, Station 19

department: ISREC

country: Switzerland

institute: Ecole polytechnique fédérale de Lausanne

description: mirRBase 12.0


title: Illumina HumanOmniZhongHua-8 v1.0 Beadchip

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

manufacture_protocol: see manufacturer's website


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: huex10st_Hs_ENSG_18.0]

first: GEO

state: MD

description:
Probe set data extracted from custom CDF;
huex10sthsensgcdf_18.0.0; Brainarray Version 18.0


title: Exiqon Human microRNA Ready-to-Use PCR, Human panel I+II

city: rasht

first: Najmeh

last: Ranji

state: Guilan

address: iran. rasht. rasht branch , islamic azad university

department: Genetics

country: Iran

institute: islamic azad university

description:
PCR array
miRCURY LNA™ Universal RT microRNA PCR kit


title: Illumina HiSeq 2000 (Steinernema carpocapsae)

status: Public on May 05 2015

organism: Steinernema carpocapsae


title: Illumina NextSeq 500 (Steinernema feltiae)

organism: Steinernema feltiae


title: Agilent-041686 Unrestricted Human miRNA Microarray (miRNA_ID version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description: GenomicBuild:  hg19:GRCh37:Feb2009

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


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [hugene10st_Hs_ENTREZG_19.0.0]

description: Brainarray: hugene10st_Hs_ENTREZG_19.0.0

relation: Alternative to: GPL6244 (Alternative CDF [official])


title: Illumina HiSeq 2000 (Pectobacterium atrosepticum SCRI1043)

organism: Pectobacterium atrosepticum SCRI1043


title: Illumina NextSeq 500 (Zea mays)

organism: Zea mays


title: Illumina MiSeq (Bacillus atrophaeus)

organism: Bacillus atrophaeus


title: LC Sciences Pig miRNA array (miRPig_18_SCA_120119)

city: Guangzhou

first: Ruisong

last: Ye

address: 483 Wushan Tianhe

institute: South China Agricultural University

organism: Sus scrofa

description:
Pig miRNAs microarray includes all porcine miRNAs deposited in miRBase 18.0 and designed sequences as miRNA microarray probes.On  the  microfluidic chip,  each  detection  probe consisted  of  a  chemically  modified  nucleotide  coding  segment complementary to target  microRNA (from  miRBase, http://microrna.sanger.ac.uk/sequences/)or other RNA  (control or customer definedsequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.The detection probes  were made by in situ synthesis using PGR (photogenerated reagent)chemistry
In detail, miRBase 18.0 collected a total of 257 porcine miRNAs (255 miRNAs according to its sequence). We added 100 probes (probes labelled with prefix 'Y-') according to our previous reports.


title: Illumina NextSeq 500 (Steinernema carpocapsae)


title: Illumina NextSeq 500 (Saccharomyces cerevisiae BY4741)

status: Public on May 03 2015

organism: Saccharomyces cerevisiae BY4741


title: Illumina Genome Analyzer IIx (Phaeodactylum tricornutum)

status: Public on May 04 2015

organism: Phaeodactylum tricornutum


title: Agilent-022565 Human Thal array v1 tiling array (Feature number version)

city: Seattle

first: Daniel

last: Sabath

state: WA

department: Laboratory Medicine

institute: University of Washington

organism: Homo sapiens

description:
Thalassemia array: HD tiling of alpha and beta globin loci (60 bp spacing). Remainder of chr11 and chr16 tiled at lower density. Genome tiled at very low density (1000 probes)

Arrays of this design have barcodes that begin with 16022565 or 2522565.

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.

Genome build: hg18.


title: Agilent-027438 Yeast S-Y SNP v1 [Probe Name Version]

city: Durham

first: Thomas

middle: D

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

organism: Saccharomyces cerevisiae

description:
Whole genome SNPs between S288c and YJM789. Both Watson and Crick strands represented as well as both probes specific to both strains.

In the labels of the oligonucleotides 'SF', 'SR', 'YF' and 'YR' refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. 'S' and 'Y' indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. 'F' and 'R' indicate whether the orientation (5' to 3') is identical to the orientation in SGD ('F' standing for forward) or opposite to that shown in SGD ('R' for reverse). Thus, 'F' and 'R' have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the 'F' orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830).

Arrays of this design have barcodes that begin with 16027438 or 2527438.

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: GPL20143 (Feature Number Version)


title: Illumina HiSeq 2500 (Monodelphis domestica)

organism: Monodelphis domestica


title: Agilent-031063 Pseudomonas aeruginosa PAO1 NC_002516 and bacteriophage PaP3 4X44K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism:
Bruynoghevirus PaP3
Pseudomonas aeruginosa PAO1

description:
Arrays of this design have barcodes that begin with 16031063 or 2531063.

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

The ID column represents the Agilent Probe Name.

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

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


title: Agilent-027438 Yeast S-Y SNP v1 [Feature Number Version]

relation: Alternative to: GPL20144 (Probe Name Version)


title: [HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate [CDF: HTHGU133PlusPM_Hs_ENST_19.0.0]

description:
This platform is identical to GPL13158 but a custom cdf environment was used to extract data.
GRCh38

manufacture_protocol: see manufacturer's web site


title: AB 5500xl-W Genetic Analysis System (Homo sapiens)


title: LC_MRA-2001_USA_130918

status: Public on May 02 2015

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Ovis aries

manufacture_protocol: Custom sheep miRNA microarray targeting the mature miRNAs of Ovis aries. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) and sequences obtained by next-gen sequencing or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: [GMH2006a530238N] Affymetrix Francisella Array

city: Hannibal

first: Siva

middle: Tej

last: Sarva

state: Missouri

address: 6500 Hospital Dr

department: Division of Pulmonary Critical Care

institute: Hannibal Regional Medical Group

organism: Francisella


title: miRCURY LNA microRNA Array (miRBASE 14.0; lot 31057)

status: Public on May 01 2015

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: See manufacturers website


title: Illumina HiSeq 2500 (Candida albicans; Streptococcus gordonii)

last: GEO

organism:
Streptococcus gordonii
Candida albicans


title: Illumina HiSeq 2500 (Streptococcus gordonii)

organism: Streptococcus gordonii


title: Agilent-061990 Genotypic S.pneumoniae R6 8x60K GE MicroArray (Feature Number version)

status: Public on Dec 29 2014

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

organism: Streptococcus pneumoniae R6

description:
Streptococcus pneumoniae R6 Nimblegen to Agilent Conversion

Arrays of this design have barcodes that begin with 16061990 or 2561990.

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-036717 ARO_Cucumber60deg_45k

city: Rishon Le-Zion

first: Ron

last: Ophir

address: Hamacabim St.

department: Fruit Tree Sciences

country: Israel

institute: Agricultural Research Organization - the Volcani Center

organism: Cucumis sativus

manufacture_protocol: CGH (SurePrint G3 Custom CGH+SNP, 4x180K)


title: Agilent-030142 ARO_Ophir_Egrandis_expression_18k

organism: Eucalyptus grandis

description: Custum made Agilent expression array of 18K probes, designed based on eucalyptus version 1 array of 44K probes. A detailed description is described in a previous study (Abu-Abied M et al. Plant journal). Briefly, 71,208 contigs published in Novaes et al., 2008 study was run against public databases databases [e.g. NR (http://www.ncbi. nlm.nih.gov/), Arabidopsis (http://www.arabidopsis.org), proteins of other plants at TAIR (http://www.arabidopsis.org), PlantGDB (http://www.plantgdb.org) and UniRef (http://www.ebi.ac.uk) at EBI] to define the orientation. Orientation of contigs that had no hit was defined by either existence of poly-A or by discovering the ORF. Probes from each contig was designed by Tm optimizing using OLIGOWIZ (Wernersson and Nielsen, 2005). In version a subset of 18K probes were taken with a first priority for the probes that were found statistically significant in Abu-Abied M et al. Plant journal.


title: NimbleGen Olive 37.5K array v1.0 [100323_Oeuro_CB_EXP]

status: Public on Nov 09 2013

city: Vairao

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

organism: Olea europaea

description:
design name: 100323_Oeuro_CB_EXP
design id: 11695

manufacture_protocol: Design and manufacture of the EST Olive Array was by Roche NimbleGen (Madison, WI, USA), using a 12-plex 135K format and the corresponding settings for this format.


title: Illumina Genome Analyzer IIx (Arabidopsis lyrata)

status: Public on Apr 01 2013

organism: Arabidopsis lyrata


title: Affymetrix HG-U133_PLUS_2[CDF: HGU133Plus2_Hs_ENTREZG_14.1.0]

status: Public on Jun 04 2014

city: Bethesda

last: admin

institute: NCBI/NLM/NIH

description: This is identical to GPL570 but a custom cdf environment was used to extract data.

manufacture_protocol: see the Affymetrix website


title: Fluidigm mouse RT-qPCR for early lineage markers and chromatin modifiers

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

organism: Mus musculus

description: Set of 192 RT-qPCR primers for early lineage markers and chromatin modifiers

manufacture_protocol: 96.96 dynamic array


title: Agilent-041686 Unrestricted Human miRNA Microarray (miRBase release 19 Feature Number version)

status: Public on Dec 10 2013


title: Bio-rad Cucumis sativus

city: Hang zhou

first: Jie

last: Wang

state: Zhe jiang province

address: Yu hangtang road 388 of West Lake District

department: Horticulture

institute: Zhejiang university

description:
CFX96TM  optics module
C1000TM thermal cycler
Bio-rad laboratories, lnc.  CFX96TM  Real-time system


title: Agilent-018073 Custom Brassica 60-mer two-color microarray

status: Public on May 03 2009

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

organism: Brassica


title: JCVI PFGRC Streptococcus gordonii 16K v1 array designed primarily based on strain Challis

status: Public on Jul 01 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

description: This set includes 2076 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: QSG, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_14.1.0]

status: Public on Jun 17 2011

address: 9000 Rockville Pike

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Agilent-021365 SurePrint G3 Human CNV Microarray 2x400K (Feature Number version)

status: Public on Mar 10 2010

last: Agilent Technologies

description:
Agilent's SurePrint G3 Human CNV Microarray, 2x400K

Arrays of this design have barcodes that begin with 16021365 or 2521365.

Data table annotations based on build hg18:NCBI36:Mar2006.

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 Genome Analyzer IIx (Caenorhabditis elegans)

status: Public on Jun 27 2011

organism: Caenorhabditis elegans


title: Illumina HumanRef-8 WG-DASL v3.0

status: Public on Apr 13 2009

city: San Diego

last: Illumina Inc.

institute: Illumina Inc.

organism: Homo sapiens

description:
The Whole-Genome DASL® Assay enables sensitive, reproducible, cost-effective gene expression profiling of low-abundance and partially degraded RNA, such as that found in formalin-fixed, paraffin-embedded (FFPE) samples. Over 24,000 targets can be analyzed at once. The Whole-Genome DASL Assay combines the proven DASL (cDNA-mediated Annealing, Selection, and Ligation) Assay and the HumanRef-8 Expression BeadChip currently used in Illumina’s Direct Hybridization Expression Assays to create an accurate, easy-to-use, higher multiplex assay. Each BeadChip contains eight arrays for simultaneous processing of eight samples. Chosen targets provide genome-wide transcriptional coverage of well-characterized National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq Build 36.2, Release 22) genes.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

relation: Alternative to: GPL16807 (gene-centered version)


title: Agilent-028279 SurePrint G3 Rat GE 8x60K Microarray (Probe Name version)

status: Public on Jan 03 2012

city: Palo Alto

institute: Agilent Technologies

organism: Rattus norvegicus

description:
SurePrint G3 Rat GE 8x60K Microarray

Arrays of this design have barcodes that begin with 16028279 or 2528279.

*** 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 GPL14797

relation: Alternative to: GPL14797 (Feature Number version)