title: Halobacterium tiling array Agilent 015962

status: Public on Jun 24 2009

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

country: USA

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

technology: in situ oligonucleotide

distribution: custom-commercial

first: David

middle: J

last: Reiss

first: Nitin

middle: S

last: Baliga

manufacture_protocol: see http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494 for details


title: NimbleGen Halobacterium 385K tiling array

description:
50mer oligo probe every 13nt.
Native NimbleGen files (ndf, pos) are linked below as supplementary files.

distribution: commercial

first: Marc

middle: T

last: Facciotti

manufacture_protocol: see http://www.nimblegen.com/technology/manufacture.html for details


title: [HG_U95D] Affymetrix Human Genome U95D Array

status: Public on Mar 11 2002

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Homo sapiens

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95).
Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent approximately 50,000 EST clusters.

Keywords = high density oligonucleotide array

manufacture_protocol: see manufacturer's web site


title: [Hu35KsubA] Affymetrix Human 35K SubA Array

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

Has 35714 entries and was indexed 29-Jan-2002.

Keywords = high density oligonucleotide array


title: [Hu35KsubD] Affymetrix Human 35K SubD Array

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

Has 35714 entries and was indexed 29-Jan-2002.


title: [Ye6100SubA] Affymetrix Yeast Genome 6K SubA Array

status: Public on May 14 2002

organism: Saccharomyces cerevisiae

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

Affymetrix GeneChip Yeast Genome 6K SubA Array Ye6100subA.
Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time.

Annotations derived from Affymetrix 'Ye6100subA Probe Set Description' file (31 KB, 3/28/03)

Keywords = Yeast


title: SMD Print_745 Mycobacterium tuberculosis

status: Public on Jun 22 2009

city: Aurora

first: Martin

middle: I

last: Voskuil

state: CO

department: Microbiology

institute: University of Colorado Denver

organism: Mycobacterium tuberculosis

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: [Ecoli] Affymetrix E. coli Genome Array

organism: Escherichia coli K-12

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

Has 7312 entries and was indexed 29-Jan-2002.
Contains probes for more than 4,200 known open reading frames of E. coli.  Also contains probe sets for stable RNA species as well as intergenic regions that do not correspond to known ORFs.
Sequence information for probes corresponds to the M54 version of E. coli Genome Project database at the University of Wisconsin.  Sequences corresponding to both characterized genes and those whose function is unknown can be identified according to the numbering convention used by the E. coli Genome Project database.
Keywords = high density oligonucleotide array


title: [RT_U34] Affymetrix Rat Toxicology U34 Array

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

Has 1031 entries and was indexed 29-Jan-2002
Contains a relevant set of toxicology genes selected from published scientific literature and in collaboration with pharmaceutical toxicologists.
Includes probes for >850 genes and EST clusters selected from Build 34 of the UniGene database.
Specific full-length sequences were selected based on their known relevance to a toxic or stress-related response.  EST clusters were selected basedon their homology to these known genes. UniGene clusters are analyzed by an exemplar sequence that is the most complete and most 3' sequence in the cluster.

Keywords = high density oligonucleotide array


title: [HC_G110] Affymetrix Human Cancer Array

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

Has 2059 entries and was indexed 29-Jan-2002.
The Human Cancer G110 array enables focused and cost-effective expression studies in cancer biology. A panel of leading cancer researchers selected the specific set of 1,700 full-length human genes implicated in cancer that comprise this array. Accession numbers for sequences selected were selected from GenBank flat file release number 110.0.

Keywords = high density oligonucleotide array


title: BTI_Tomato_12800_v.CGEP

status: Public on Jun 30 2009

city: Québec

first: Jean-François

last: Dubuc

address: 2440 boul. Hochelaga

country: Canada

institute: Université Laval

organism: Solanum lycopersicum

technology: spotted oligonucleotide

description: The array consist of 32 subgrids (4 meta-rows, 8 meta-columns). Each sub-grid contains 20 rows and 20 columns

manufacturer: Center for Gene Expression Profiling (CGEP) at Boyce Thompson Institute of Plant Research

manufacture_protocol: TOM2 array were available from the Center for Gene Expression Profiling (CGEP) at Boyce Thompson Institute for Plant Research. TOM2 oligo array from tomato contain a total of 12800 elements or approximately 11860 unique elements. Sixty-nine oligonucleotides sequences from unigenes were synthesized by Operon (Operon biotechnologies, Hunstville, AL). Oligos were re-suspended in 12 uL of spotting buffer (3X SSC), and were spotted on Ultra Gaps Coated Slides (Corning, Lowell, MA) using a MicroGrid Pro arrayer (BioRobotics Inc., MA) with 32 MicroSpot2500 printing pins. Temperature and humidity inside the arrayer were maintained at 18-21°C and 35-45% RH, respectively. Oligos were fixed to the slide by 2-h incubation at 80°C.


title: [Hu35KsubC] Affymetrix Human 35K SubC Array


title: [Hu35KsubB] Affymetrix Human 35K SubB Array


title: [U133_X3P] Affymetrix Human X3P Array

status: Public on Jul 20 2004

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip X3P Array was designed specifically for whole-genome expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples, and is now available via the GeneChip Made-to-Order program.

Resulting from a collaboration between Affymetrix and Arcturus, this array is optimized as part of a system solution together with the Paradise Reagent System from Arcturus for expression analysis of FFPE samples.

FFPE samples introduce unique challenges for microarray analysis, including potential fragmentation and chemical modification of RNA molecules. In order to overcome these challenges, the Paradise Reagent System was developed to provide RNA isolation and amplification reagents optimized for FFPE samples. In addition, the X3P Array is designed to focus on interrogating sequences located closer to the 3' end of the transcripts compared with standard GeneChip arrays. Together, the reagents and array accommodate the characteristics of the FFPE RNA samples, enabling genome-wide profiling.

The target sequences on the X3P Arrays are identical to those used for designing the Human Genome U133 Plus 2.0 Array, for a total of 47,000 transcripts with 61,000 probe sets, although the probes on the two types of arrays are significantly different.

As a result of the modification to the probe selection criteria, the majority of the probe sets on the X3P arrays are selected from the 300 bases at the most 3' end of the transcripts. This is different from the standard Affymetrix design strategy which selects probe sets within the region of 600 bases proximal to the 3' ends.

To select probes for the 47,000 transcripts, it was not possible to identify high-performance probe sets within the shorter 300 base probe selection region for approximately 4,000 transcripts. For these transcripts, two sets of probes are represented on the arrays: 1) the original probe sets from the standard HG-U133 Plus design are replicated on the X3P arrays, and 2) the new, more 3' probe sets are also included although they fell below the minimum probe score selection threshold.

In addition, fewer than 200 transcripts from the HG-U133 Plus design are only represented by the HG-U133 Plus probe sets, where no probe sets within the smaller (300 bps) probe selection region could be found.

Annotations derived from Affymetrix CSV file dated 6/23/2004


title: Zoarces viviparus validation microarray

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

organism: Zoarces viviparus

description: This microarray contains 117,316 probes used to evaluate the transcript assembly described in Kristiansson et al 2009.

manufacturer: Department of Zoology, University of Gothenburg / Febit gmbh, Heidelberg, Germany

first: Noomi

last: Asker

first: Lars

last: Förlin

first: Joakim

last: Larsson

manufacture_protocol: Probes were designed according to Kristiansson et al 2009. Oligonucleotides were then synthesized in situ on one single biochip using the 5’ standard synthesis set for Geniom Instrument (http://www.febit.com/go/en/).


title: Spodoptera frugiperda 20k (v2-inra)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

organism: Spodoptera frugiperda

first: Frederique

last: Hilliou

manufacture_protocol: spotted microarray


title: USYD Dermatology Compugen Mouse 22K

status: Public on Jun 29 2009

city: Sydney

first: Michael

middle: Peter

last: Stapelberg

state: NSW

address: The University of Sydney

department: Medicine

country: Australia

institute: The University of Sydney

organism: Mus musculus

manufacture_protocol:
Array Design Name: Ramaciotti Centre CGenMm22K
Lot number: CGenMm22K_B1
Platform type: spotted
Array provider (source): The Clive and Vera Ramaciotti Centre for Gene Function Analysis
Surface type: glass
Surface type name: Schott Nexterion Slide E (Epoxy)
Physical dimensions: 75 mm x 25 mm
Total number of elements: 22464
Reference system (with slide in vertical orientation): Number of subarrays: 48Vertical subarrays: 12Horizontal subarrays: 4Vertical features/subarray: 20Horizontal features/subarray: 24Feature size (µm): 100Feature separation (µm): 180Reference Mask provided?: Yes
Pin configuration: 12X4
Production date: 10/5/05.
Process date: Slides require blocking to be carried out immediately prior to hybridisation.
Production protocol: Contact pin
Element type unique ID: GenBank
Simple or composite: Simple
Element type: 60 mer oligonucleotide
Single/double stranded: Single stranded (sense)
Element generation protocol: Amino-modified oligonucleotide synthesis
Gene set provider:	Compugen plus Amersham Lucidea Universal ScoreCard
PCR primers: NA
Sequence information: NA
Oligo length: 60 mer


title: Ryerson University E-coli O157:H7 MWG 7K array version 1

status: Public on Jun 26 2009

city: Toronto

first: Debora

last: Foster

state: Ontario

address: 350 Victoria Street

department: Chemistry and Biology

institute: Ryerson University

organism: Escherichia coli

first: Belinda

last: House

first: Nita

last: Prayitano

first: Richard

middle: W

last: Mair

first: Julianne

middle: V

last: Kus

first: Lynne

last: Que

first: Victor

last: Gannon

first: Dennis

middle: G

last: Cvitkovitch

last: Barnett Foster

manufacture_protocol:
Corning Ultra-Gap II slides (Corning, Acton, MA) were spotted with the MWG E. coli O157:H7 array set (MWG Biotech). The MWG array consists of 6167 50-mer oligonucleotides covering the genomes of E. coli K-12 (MG1655) and E. coli O157:H7 strains Sakai (RIMD 0509952) and EDL933 (ATCC700927), with each gene spotted twice.
Reference: BMC Genomics 2007, v.8: 121


title: Univ Colorado Denver Mycobacterium tuberculosis 4.6K Operon Microarray

first: Ryan

middle: William

last: Honaker

organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

manufacturer: Voskuil laboratory, University of Colorado Denver

first: Martin

last: Voskuil

manufacture_protocol:
1.Oligos (purchased from Operon) are arrayed in Whatman 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Oligos are suspended in 3xSSC to 20 uM and centrifuged at 500 rpm for 2 minutes.
3. Plates are stored at 4oC overnight.
4. Incubate at RT for 30 minutes and shake for 5 min to aid resuspension of DNA.
5. Centrifuge plates at 500 rpm for 2 minutes.
6. Remove seals.
7. Print.
8. After completion of print, allow slides to dry through passive evaporation in a protected environment.


title: ViaLactia Biosciences custom bovine array 22k version 1b

city: Auckland

first: Matt

middle: D

last: Littlejohn

address: PO Box 109-185 Newmarket

country: New Zealand

institute: DairyNZ

organism: Bos taurus

description: This array is an early version of the now commercially available Agilent Bos taurus 44k array (Agilent design ID 015354).

first: Klaus

last: Lehnert

first: Hamish

last: Ward

manufacture_protocol: 325,000 EST, mRNA, and CDS region sequences for Bos taurus genes were retrieved from GenBank, and supplemented with paired 5'- and 3'-reads from 100,000 ESTs obtained from normalized bovine fetal brain, lactating and non-lactating mammary gland cDNA libraries. After repeat masking, sequences were clustered by pairwise-comparison using Paracel Transcript Assembler (Paracel, Pasadena, CA, USA) to reduce redundancy, and the resulting clusters were mapped to genes predicted from the 2.1 assembly of the bovine genome. Gene-specific cluster sequences were then supplemented with novel transcript sequences predicted by the NCBI RefSeq project (http://www.ncbi.nlm.nih.gov/RefSeq/). Probe sequences (60-mer) targeted towards the 3' regions of the transcripts were designed by Agilent Technologies. 21,495 unique probe sequences were selected for array manufacture by in-situ synthesis.


title: [Mu11KsubB] Affymetrix Murine 11K SubB Array

last: Affymetrix

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

Has 13179 entries and was indexed 29-Jan-2002.
Keywords = high density oligonucleotide array


title: UofIL_RUMFLA_FD1_13K

city: Urbana

first: Bryan

middle: A

last: White

state: IL

address: 1207 W. Gregory Drive

department: Animal Sciences

institute: University of Illinois

organism: Ruminococcus flavefaciens FD-1

manufacturer: University of Illinois W.M. Keck Center for Comparative and Functional Genomics

manufacture_protocol: 6,144 PCR-amplified clone inserts from the RF03 library were spotted in duplicate onto aminosilane coated glass slides using a Gene Machines OmniGrid 100 Microarrayer.


title: [AG] Affymetrix Arabidopsis Genome Array

organism: Arabidopsis thaliana

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

Has 8297 entries and was indexed 29-Jan-2002.
The sequences used to develop this array were obtained from GenBank in collaboration with Novartis Agriculture Discovery Institute, Inc. Probes were synthesized in situ.
Eighty percent of the genes represented are predicted coding sequences from genomic BAC entries. Twenty percent are high quality cDNA sequences. Also contains >100 EST clusters, sharing homology with predicted coding sequences from BAC clones.

Keywords = high density oligonucleotide array


title: UMD Metarhizium anisopliae V1.0

status: Public on Jun 25 2009

city: College Park

first: Sibao

last: Wang

state: MD

address: Baltimore Avenue

department: Entomology

institute: University of Maryland

organism: Metarhizium anisopliae

manufacturer: University of Maryland Biotechnology Institutes in Shady Grove, MD

first: Monica

last: Pava-Ripoll

first: StLeger

last: Raymond

manufacture_protocol: The construction of the cDNA microarrays used in this study has been previously described (Wang et al., 2005). This array harbors PCR amplified fragments from the unique cDNA clones from M. anisopliae var. anisopliae ARSEF 2575 and a few genes from M. anisopliae var. acridum ARSEF 324 absent from the libraries of ARSEF 2575. In total, 1730 amplified clones were printed in triplicates on the slides. Additional background control was provided by 30 randomly distributed spots of 3×SSC buffer. Printing, hybridization, and scanning of slides was as described before (Freimoser et al., 2005).


title: [Chicken] Affymetrix Chicken Genome Array

status: Public on Dec 01 2005

organism: Gallus gallus

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

Sequence information for the GeneChip Chicken Genome Array can be used to study gene expression of 33,457 chicken and viral transcripts. Species covered include Gallus gallus (chicken) and 17 avian viruses. Sequence information for this array includes public content from GenBank®, UniGene (Build 18; 15 May 2004), and Ensembl (version 1, released May 2004). Probe sets on the array were designed with 11 oligonucleotide pairs to detect each transcript.

relation: Alternative to: GPL10234 (Alternative CDF)


title: [HT_MG-430B] Affymetrix HT Mouse Genome 430B Array

status: Public on Jun 23 2009

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The probe sets were selected from sequences derived from GenBank®, dbEST and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute Center for Genome Research (MSCG, April 2002).

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the array. Eleven pairs of oligonucleotide probes, including a perfect match and mismatch probe, are used to measure the level of transcription of each sequence represented on the GeneChip® HT Mouse Genome 430 Array Plate Set.


title: [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array

status: Public on Jun 30 2004

organism: Xenopus laevis

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The Affymetrix GeneChip Xenopus laevis Genome Array can be used to study gene expression of over 14,400 Xenopus laevis transcripts. Sequence information for this array was selected from the following public data sources: GenBank (release 135.0, April 2003), dbEST (June 2003), and UniGene (Build 36, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript.

This array was designed in collaboration with representative members of the Xenopus community and the National Institutes of Health. More information on the design of this array can be found at www.xenbase.org

Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences.


title: CAGE Lab - Head and Neck carcinoma cDNA microarray

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

organism: Homo sapiens

manufacturer: CAGE Lab - Department of Biochemistry, Institute of Chemistry, University of São Paulo

middle: M

first: Jucimara

last: Colombo

manufacture_protocol:
We selected 136 genes previously identified by the Head and Neck Annotation Consortium (Reis et al., 2005, Cancer Research 65:1693) to be spotted in the cDNA microarray. The criteria for selection of the genes were based on known genome mapping information. Thus, genes that map to loss or gain regions involved in head and neck carcinogenesis, according to Knuutila et al. (Knuutila et al., 2000, Am J Pathol 157:689) were selected.
Complementary DNA of the Hep2 (Human laryngeal carcinoma) cell line served as template for the amplification of probes from microarray spotting. Gene-specific primers for PCR were designed using the Primer 3.0 program.
In brief, for the PCR, 1 uL cDNA was mixed with 2.5 uL 10x buffer, 1 uL PCR primer (10 pmol/L), 4 uL dNTPs (1.25 mM), 0.75 uL MgCl2 (50 mM) and 0.2 uL Taq DNA Platinum (Invitrogen). PCR conditions were: 94ºC for 4 min, followed by 35 cycles at 94ºC for 30 s, 60ºC for 1 min and 72ºC for 1 min.
The products obtained by PCR had the expected sizes and have average length of 600 bp. From all products, 5uL were fractionated by electrophoresis through a 1% agarose gel for size verification, and the remaining 95uL were purified by filtration on Multiscreen plates (Millipore cat. # MAFB NOB 50). cDNA samples were diluted 1:1 in DMSO and spotted onto silane-coated, reflective Type-7 glass slides (GE Healhcare), using a Generation III microarray spotter robot (GE Healhcare). Twelve replicates of 4 different plant/bacterial DNA fragments with no similarity to human sequences were evenly distributed along the slide to serve as negative controls of nonspecific hybridization (Lucidea ScoreCard − GE Healthcare). Following spotting, cDNAs were fixed to the slide surface by UV cross-linking (500 mJ) and kept in a low-humidity environment until use.
Based on an informatics analysis of the HN transcriptome to identify candidates for LOH in Head and Neck tumors, an additional set of 196 cDNA clones were included in the array, comprising partial sequences of protein-coding transcripts (123 sequences), as well as of transcripts mapping to intronic (53 sequences) or intergenic regions of the genome (20 sequences). The original sequencing clone collection was stored frozen in bar-coded 96-well plates, and the selected clones were re-arrayed in an automated robotic operation. cDNA fragments were generated from these clones by PCR amplification with universal primers, purified by filtration and spotted as described above. Each probes was deposited 3-4 times, in duplicate, in the arrays. Thus, 6 to 8 replicates of each probe are spotted in the microarrays.


title: Bacillus cereus ATCC 14579, 1st design, Agilent 2X11K

city: Wageningen

first: Heidy

last: den Besten

address: Bomenweg 2

country: Netherlands

institute: Wageningen University

organism: Bacillus cereus ATCC 14579

first: Menno

last: van der Voort

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

first: Douwe

last: Molenaar

manufacture_protocol:
Agilent manufacture protocol.
Agilent uses its inkjet technology to print oligos onto glass slides.


title: CERI Rat 6.7K ToxArrayIII

status: Public on Jun 21 2009

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

first: Kouji

last: Nakayama

first: Hideki

last: Miyaura

first: Fumiyo

last: Saito

first: Kayo

last: Sumida

first: Koichi

first: Masaru

last: Sekijima

first: Yoshikuni

last: Yakabe

first: Tomoyuki

last: Shirai

manufacture_protocol:
See manufacturer's website.
http://www.ngk.co.jp/english/products/life/index.html


title: NHGRI_HS_Exp_Tile_3

status: Public on Jun 20 2009

city: Bethesda

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description:
NHGRI Human 17q/20q 60 mer Expression Tiling Array 3
UCSC HG16

first: Paul

last: Meltzer

first: Yidong

last: Chen

first: Yuan

last: Jiang

first: Tyra

last: Wolfsberg

first: John

last: Pearson

manufacture_protocol: See manufacture's website


title: [HT_MG-430A] Affymetrix HT Mouse Genome 430A Array

last: Affymetrix


title: Bacillus cereus ATCC 14579, 2nd design, Agilent 2X11K

first: Heidy

last: den Besten

first: Menno

last: van der Voort

first: Roy

last: Moezelaar

first: Tjakko

last: Abee


title: FGP_Persea americana_6K_V1.0

status: Public on Jun 18 2009

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road and Newell Drive

department: Botany

institute: University of Florida

organism: Persea americana

description: 10187 randomly arrayed probes for targeting 6068 unique Persea americana transcripts, 544 features are Agilent proprietary controls, and 75 features are negative controls.

first: Victor

last: Albert

first: Jim

last: Leebens-mack

first: Naomi

last: Altman

first: Douglas

middle: E

last: Soltis

first: Pamela

manufacture_protocol: 60 mer in situ oligonucleotide synthesis using solid phase phosphoramidite chemistry


title: NHGRI_HS_Exp_Tile_1

description:
Human 17q/20q 60 mer Expression Tiling Array 1
UCSC HG16


title: NHGRI_HS_Exp_Tile_2

description:
NHGRI Human 17q/20q 60 mer Expression Tiling Array 2
UCSC HG16


title: Gliomatosis_Homo_sapiens_725

status: Public on Jun 16 2009

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

description: The substrates used were Nexterion Slide E epoxy slides

middle: F

first: Pietro

first: Pasqualino

last: Ciappetta

manufacture_protocol: Probe set relative to all 725 gene features were designed by means of ArrayDesigner4. Probes were purchased dry in 384 well plate and resuspended in 3X SSC as spotting buffer. Spotting was performed by means of SpottArray 428 (Perkin Elmer), under humidity range of 50%-60% with optimum setted to 55%. All probes were spotted in dupplicate. After printing procedure slides were incubated in a 95% humidity chamber for 30'. After dry to 60° for 20 minutes slides were stored dry and light protected upon usage


title: Candida_albicans_ArrayII_v5

status: Public on Jun 15 2009

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

organism: Candida albicans

description: This platform has a different probe layout and different printing date than the other platforms.

first: Judith

last: Berman

first: Eric

last: Benson

first: Mark

last: McClellan

first: Anja

last: Forche

manufacture_protocol: Array production and printing were done as described for ArrayI and ArrayII platforms. Primer pairs were used to amplify Candida albicans ORFs from SC5314 genomic DNA. PCR fragments were purified on MultiScreen-PCR 96-well filtration units (Millipore, Bedford, Mass.) and were eluted in spotting buffer (3 SSC [(1 SSC is 0.15 M NaCl plus 0.015 M sodium citrate] plus 0.01% SDS). Purified PCR products were spotted in duplicate on poly-L-lysine-coated slides with a MicroGrid II (BioRobotics, Cambridge, United Kingdom). Slides were postprocessed with succinic anhydride in 1-methyl-2-pyrrolidinone (http://www.microarrays.org/protocols.html).


title: Agilent 015961 Mouse Array

city: College Station

first: Scott

last: Dindot

state: TX

address: Texas Veterinary Medical Center, 4467 TAMU

department: Veterinary Pathobiology

institute: Texas A&M University

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


title: S. cerevisiae UNC_OIRF_INT_N array

status: Public on Jun 14 2009

city: Princeton

last: Azvolinsky

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

organism: Saccharomyces cerevisiae

description: 14976 ORF and intergenic spots

manufacture_protocol: as Iyers et al.


title: JCVI Synechococcus sp. WH 8102 19K v1.0

first: Ian

last: Paulsen

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

organism: Parasynechococcus marenigrum WH 8102

technology: mixed spotted oligonucleotide/cDNA

first: Brian

last: Palenik

first: Katherine

last: Phillippy

first: Daniel

last: Johnson

manufacture_protocol: Primers were designed to yield 2142 PCR amplicons of approximately 800 base pairs, and 70-mer oligonucleotides were designed for another 389 genes that were less than 200 base pairs in length or could not be amplified by PCR.  PCR amplicons and oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer.  Each gene is represented six times on the array.  Negative controls include 50% DMSO / 50% DI water and air.  A mixture of PCR amplicons, Arabidopsis spike-in controls, and Arabidopsis 70-mer oligonucleotides were used as positive controls.  Slides were air dried for at least 30 minutes after printing.  DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker.  Slides were stored at room temperature in a dessicator.


title: PIQOR (TM) Stem Cell Microarray, mouse, antisense (596)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

description: The PIQOR (TM) Stem Cell Microarray is composed of 910 mouse specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: C. botulinum ATCC3502 strain variable region microarray v1.0

city: Atlanta

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

organism: Clostridium botulinum A str. ATCC 3502

description:
Probes represent strain variable regions in C. botulinum strain ATCC 3502.
Probes for selected genes (eg. toxin genes) were also featured on the microarray to allow detection of other serotypes/subtypes.

The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

first: Lavin

last: Joseph

first: Loretta

last: McCroskey

first: Carolina

last: Luquez

first: Susan

last: Maslanka

manufacture_protocol: Oligonucleotides (with C6 amino linker) were suspended at 50pmoles/ul in spotting buffer and spotted onto SuperEpoxy2 substrate glass slides using 946MP3 Micro Spotting Pins.


title: NHGRI Homo sapiens CGH 70mer

first: Christopher

last: Pan

description:
NHGRI Human 17q/20q 70 mer Tiling Array CGH
UCSC HG16

first: Paul

last: Meltzer

first: Yidong

last: Chen

first: Yuan

last: Jiang

first: Tyra

last: Wolfsberg

first: John

last: Pearson


title: Candida_albicans_ArrayIB

first: Anna

last: Selmecki

description: The same probes were used for this platform and all the other platforms.  This is also the same probe layout as ArrayI, just a different printing date.

first: Judith

last: Berman

first: Eric

last: Benson

first: Mark

last: McClellan

first: Anja

last: Forche

manufacture_protocol: Primer pairs were used to amplify Candida albicans ORFs from SC5314 genomic DNA. PCR fragments were purified on MultiScreen-PCR 96-well filtration units (Millipore, Bedford, Mass.) and were eluted in spotting buffer (3 SSC [(1 SSC is 0.15 M NaCl plus 0.015 M sodium citrate] plus 0.01% SDS). Purified PCR products were spotted in duplicate on poly-L-lysine-coated slides with a MicroGrid II (BioRobotics, Cambridge, United Kingdom). Slides were postprocessed with succinic anhydride in 1-methyl-2-pyrrolidinone (http://www.microarrays.org/protocols.html).


title: Candida_albicans_ntd2

description: This platform uses the same probes as the other platforms, the major difference is that there are no tandem duplicate (ntd) probes and thus a different physical layout.


title: NimbleGen Homo sapiens 384K hg18 tiling set 16

status: Public on Jun 13 2009

city: London

first: Steve

last: Best

address: 125 Coldharbour Lane

department: The James Black Centre

country: United Kingdom

institute: King's College London

first: Karin

last: Wahlberg

first: Jie

first: Helen

last: Rooks

first: Kiran

last: Jawaid

first: Fumihiko

last: Matsuda

first: Masao

last: Yamaguchi

last: Lathrop

first: Swee-Lay

last: Thein

manufacture_protocol:
NimbleGen 385K Whole-Genome Tiling Sets
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
HG18Tiling Set 16 Array 16 of 38
chr6 93,424,310 165,905,673
Arrays Per Slide: 1
Probes Per Array: 385,000
Array Size: 17.4mm x 13mm
Feature Size: 16μm x 16μm
Slide Size: 1" x 3" (25 x 75mm)


title: Agilent-021529 Human CGH Whole Genome Microarray 1x1M (G4447A) (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human CGH Whole Genome Microarray, 1x1M

*** 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 GPL8736.


title: Eisenia fetida 244K oligo test array version 4

status: Public on Jun 12 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

organism: Eisenia fetida

description:
Arrays of this design have barcodes that begin with 16020025 or 2520025.
Orientation: assume antisense orientation of target sequences
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: Eisenia fetida 244K oligo test array version 1

description:
Arrays of this design have barcodes that begin with 16020022 or 2520022.
Orientation: assuming sense
Features are numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner, i.e., 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, i.e., 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: Eisenia fetida 244K oligo test array version 3

description:
Arrays of this design have barcodes that begin with 16020024 or 2520024.
Orientation: assume sense orientation of target sequences
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: Eisenia fetida 244K oligo test array version 2

description:
Arrays of this design have barcodes that begin with 16020023 or 2520023.
Orientation: assume antisense orientation of target sequences
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: Ocimum OciChip CA010_Teagasc, Lactobacillus helveticus 2K array

city: Fermoy

first: Pawel

last: Kaleta

state: Co Cork

address: Moorepark

department: Biotechnology

country: Ireland

institute: TEAGASC

organism: Lactobacillus helveticus DPC 4571

manufacture_protocol: 50mer oligonucleotides spotted in duplicates, 2x105k


title: MacArary Karyo 4000

status: Public on Jun 11 2009

city: New York

first: Jiun

last: Kang

state: NY

address: 1130 St. Nicholas Avenue

department: Pathology

institute: Columbia University

description: The array was based on NCBI build 36.2, UCSC hg18 of the human genome and used in this study consists of 4,044 human Bac-terial Artificial Chromosomes (BACs), which were spaced approximately 1.0 Mb on average across the entire genome

first: SongJu

last: Yang

first: Kapseok

first: Jongho

first: EunHee

last: Oh

first: HyunWoong

first: JeongSun

last: Seo

manufacture_protocol:
The clones were prepared by conventional alkaline lysis
method to obtain BAC DNA. The DNA was sonicated to generate fragments of ~3 kb and then was mixed with 50% dimethyl sulfoxide spotting buffer. The arrays were manufactured using a Molecular Dynamics (Sunnyvale, CA) Generation III spotter in an eight-pin format. BAC clones were represented on an array as duplicated spots and each array was prescanned using an Axon scanner for proper spot morphology (Axon InstrumentsdMolecular Devices, Sunnyvale, CA). The array used in this study consists of 4,046 human BACs, which were spaced ~1 Mb across the whole genome.


title: Genotypic Technology's M. tuberculosis H37Rv 8x15 GE Array

status: Public on Jun 10 2009

city: Bangalore

first: Genotypic

last: Technology

state: Karnatka

address: 259, Apurva

country: India

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

description: contributor: GENOTYPIC,,TECHNOLOGY

first: GENOTYPIC

last: TECHNOLOGY

manufacture_protocol: refer to www.agilent.com


title: Nimblegen custom human chromosome 1 high density 385K oligonucleotide array

status: Public on Jun 09 2009

city: Seattle

first: Barbara

middle: J.

last: Trask

state: WA

address: 1100 Fairview Avenue N., C3-168, P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
A custom array of 385,001 isothermic oligomers representing the euchromatic portions of chromosome 1 was designed and fabricated by Nimblegen using the methods described previously (R.R. Selzer et al., Genes Chromosomes Cancer, 2005). The array was designed to maximize representation of HpaII fragments of size between 25 bp and 2500 bp. Of the 151,812 predicted HpaII fragments on chromosome 1 in that size range, 120,532 are represented on the array by at least one probe, and ~30% of these are represented by four probes.
array map file 2006-01-12_HG17_DeBustos_HpaII.ndf

first: Cecilia

last: De Bustos

first: Edward

last: Ramos

first: Janet

last: Young

first: Robert

middle: K

last: Tran

first: Uwe

last: Menzel

first: Cordelia

last: Langford

first: Evan

last: Eichler

first: Li

last: Hsu

first: Steve

last: Henikoff

first: Jan

middle: P

last: Dumanski

middle: J

manufacture_protocol: As described in R.R. Selzer et al., Genes Chromosomes Cancer, 2005


title: AH/VLA Virus Detection Array LP1 1.6K

city: Addlestone, Surrey

first: Akbar

last: Dastjerdi

address: Woodham Lane

department: Virology

institute: Animal and Plant Health Agency

organism: Viruses

first: R

last: Gurrala

first: A

first: N

last: Johnson

first: J

last: Nunez-Garciac

first: S

last: Grierson

first: F

last: Steinbach

first: M

last: Banks

manufacture_protocol:
Oligos were synthesised commercially and spotted to Epoxy-coated glass slides using a Migrogrid II robot (Biorobotics) using previously published protocol [1]
1. Burton, J.E., et al., Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes, 2005. 19(5): p. 349-57.


title: Rosetta/Merck Human P4 Array3

first: Amit

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains full length probes

first: John

last: Castle

manufacture_protocol: see Merck's web site


title: Wellcome Trust Sanger Institute human chromosome 1 tile path 2K CGH array version 3

first: Barbara

last: Trask

description:
The chromosome 1 tile path array clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. The array has 24 subarrays (6 rows by 4 columns), each subarray consisted of 16 rows by 16 columns.
Map file new_Chr1Map_brief.txt can be used to process raw data

first: Cecilia

last: De Bustos

first: Edward

last: Ramos

first: Janet

last: Young

first: Robert

manufacture_protocol: As described in Fiegler H et al. Genes Chromosomes Cancer 36:361-374, 2003


title: Rosetta/Merck Human P4 Array2


title: Rosetta/Merck Human P3 Array6


title: Rosetta/Merck Human P3 Array3


title: Rosetta/Merck Human P3 Array5


title: Rosetta/Merck Human P3 Array4


title: Rosetta/Merck Human P3 Array2


title: SAGE:17:NlaIII:Oryza sativa

status: Public on Jun 08 2009

last: GEO

organism: Oryza sativa

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Oryza sativa using NlaIII as an anchor enzyme.

distribution: virtual


title: NimbleGen Human chromosome 8q24 385K tiling array

first: Mark

last: Pomerantz

address: 44 Binney St.

department: Medical Oncology

description:
RNA expression at chromosome 8q24 in human colon.
Genome build: NCBI BUILD 35 (HG17).
Native NimbleGen files linked below as supplementary files.

first: Matthew

last: Freedman

middle: R

last: Manak

manufacture_protocol: see manufacturer's website


title: Radboud University Mus musculus 385K Tiling array [2006-07-17_MM8Tiling_Set38]

status: Public on Jun 06 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

organism: Mus musculus

description:
DESIGN_ID: 4109
DESIGN_NAME: 2006-07-17_MM8Tiling_Set38
Set 38 of 38. Whole mouse genome (mm8 from UCSC) tiled at 100 bp spacing excluding repeat masked regions. Design contains random probes with GC content between 9-34%.
Native NimbleGen files (ndf, pos) are linked below as supplementary files.

manufacture_protocol: Nimblegen Systems Inc


title: Rosetta/Merck Human P3 Array1


title: Winzeler Lab Plasmodium 17k array (PlasmoFBa520596)

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

state: CA

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

organism:
Plasmodium berghei
Plasmodium falciparum

description: The custom chip definition CDF file and probe sequence files are linked below as supplementary files.

first: Stephan

last: Meister

first: Anat

last: Caspi

first: David

middle: S

last: Roos


title: SMD Print_798 Homo sapiens

status: Public on Jun 04 2009

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

institute: Stanford University

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: UBEC Array3, condensed version

status: Public on Jun 03 2009

city: Ås

first: Birgitte

last: Moen

address: Osloveien 1

country: Norway

institute: Nofima Mat

organism: Escherichia coli

manufacturer: UBEC, School of Biosciences, University of Birmingham, Birmingham, UK

first: Chrystala

last: Constantinidou

first: Jon

middle: L

last: Hobman

first: Charles

middle: W

last: Penn

first: Mala

last: Patel

first: Antony

last: Jones

manufacture_protocol:
The 70-mer oligonucleotide array was constructed, containing 6112 oligonucleotides that sampled chromosomal genes identified in the genome sequences of E. coli strains K-12 MG1655, O157:H7 VT2 Sakai, and O157:H7 EDL933 and plasmid genes from the two genome-sequenced O157:H7 strains (the Operon Array Ready E. coli Oligonucleotide™ set 1.0, Qiagen- Operon, Hilden, Germany). 12 positive and 12 negative control oligonucleotides were also included. The oligonucleotides were resuspended in Corning Pronto! buffer and printed on to Corning UltraGAPS™ slides (Corning B.V Life Sciences, Schiphol-Rijk, Netherlands ) using a Biorobotics Microgrid TAS array printer. Amersham Lucidea Universal Scorecard™ controls (GE Healthcare, Little Chalfont, UK) were printed in each subarray. Slides were desiccated under vacuum for 48 hours and then U.V. cross-linked with a dose of 600mJ using a Stratalinker (Stratagene limited, U.K.). Slides were stored under desiccating conditions in the dark until use.
This is a condensed array version of GPL3051


title: South Dakota State University custon Vitis bud 10K cDNA array version 1

city: Brookings

first: Kathy

last: Mathiason

state: SD

address: NPB 201 Box 2140A

department: Horticulture, Forestry, Landscape, Parks

institute: South Dakota State University

organism:
Vitis vinifera
Vitis riparia

description: 7920 Vitis vinifera cv. 'Perlette' clones (1248 natural dormancy cycle library,1920 young bud library, 2400 hydrogen cyanamide library, and 2352 control library); 1141 Vitis riparia Michx. (475 paradormant library, 666 endodormant library)

manufacturer: University of Arizona Department of Plant Science

first: Anne

middle: Y

last: Fennell

last: Galbraith

first: Etti

last: Or

manufacture_protocol: cDNAs spotted in SSC using a GeneMachines 'OmniGrid 100'


title: Clostridium beijerinckii NCIMB 8052 Spotted Oligonucleotide Array v1

status: Public on Jun 02 2009

city: Urbana

first: Zhen

last: Shi

state: IL

address: 1206 West Gregory Drive

department: Institute for Genomic Biology

institute: University of Illinois

organism: Clostridium beijerinckii NCIMB 8052

description:
The draft genome sequence assembly of Clostridium beijerinckii (whole genome shotgun [WGS] project accession AALO00000000) was used as a source of the genes used in this study. Note, this WGS project has been superceded by the complete genome in (non-WGS) GenBank record CP000721.
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacturer: University of Illinois Functional Genomics Center Microarray Facility

first: Hans

last: Blaschek

manufacture_protocol: An oligonucleotide of 70 bp was designed as a probe specific for each gene.  Each probe was made on the forward strand of the gene.  A probe was selected based on global optimization from all combinations of 70-mer within the target sequence by scoring simultaneously for a set of criteria including melting temperature, presence of hairpin/secondary structure, presence of low-complexity sequence and sequence specificity with respect to other genes.  Sequence specificity was examined by sequence alignment using BLAST to ensure that the selected probe is different from all other sequences in the set beyond a certain value.  All 70-mer probes have very similar melting temperature of ~65 oC.  The oligonucleotides were synthesized (Invitrogen) and printed as duplicates onto glass slides.  The slides were hybridized using probes generated by an aminoallyl-labeling and Cy dye-coupling procedure adapted from a TIGR protocol.  Hybridized slides were scanned on an Axon Microarray Scanner.  Features were extracted using GenePix Pro.


title: Avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA) version 2

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

organism: Gallus gallus

manufacturer: Lab of Dr. Hyun Lillehoj, Animal Parasitic Diseases Laboratory, ARS, US Department of Agriculture

manufacture_protocol: The microarray was constructed from 10,162 spot elements selected from the previously prepared IEL clones (Min et al., 2005) and the immune-related genes from lipopolysaccharide (LPS)-activated macrophage (HD11) cDNA library (Min et al., 2003) as well as the direct PCR clones of several cytokines and chemokines (Min et al., 2005). PCR products of the ESTs were dried and resuspended in 3X SSC, 0.01% SDS, followed by spotting in duplicate  onto MicroMax glass slides (Perkin Elmer, Boston, MA) using an OmniGrid Accent spotter (GeneMachines, San Carlos, CA).  The elements were organized into duplicated 24 subarrays, each as a 21 x 21 spot grid.  The PCR products were fixed by UV cross-linking, followed by assessment of spotting quality by staining with SYBR-Green II according to the manufacturer's protocol (Invitrogen, Carlsbad, CA).  Greater than 90% of the spots possessed an verage diameter of 150-200 µm.


title: Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2

city: Davis

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

technology: other

description: The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. High-throughput sequencing was performed at 454 Life Sciences using the 454 pyrosequencing method (Margulies et al., 2005) using 5' and 3' adapter oligonucleotides.  Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2.  The total number of sequence reads were respectively 70406 and 191682.

first: Cameron

last: Johnson

first: Alex

last: Adai

first: Anna

last: Kasprzewska

first: Kristin

last: Tennessen

first: John

last: Fernandes

first: Guo-Ling

first: Virginia

last: Walbot

first: Vicki

last: Vance

first: Lewis

last: Bowman

manufacture_protocol: see manufacturer website www.454.com


title: Agilent custom 244K oligo RNA Binding Protein microarray v2

status: Public on Jun 07 2009

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

organism: synthetic construct

description: This custom microarray consists of probes representing two complete sets of (1) all possible 10-base sequences (contained within longer unstrctured RNAs) and (2) all possible 7- and 8-base loop sequences in the context of RNA hairpins containing unique 10 base pair stems. An RNA pool is synthesized from on the array and subsequently stripped from the array and PCR-amplified to create a dsDNA pool. This pool is then used as a template for in vitro T7 RNA polymerase-mediated RNA transcription to generate an RNA pool used for pull-down experiments using GST-tagged RNA binding proteins. The RNAs pulled-down by each RNA-binding protein are then labelled with a fluorophore and hybridized back onto the array, along with the total pool.

first: Debashish

last: Ray

first: Hilal

last: Kazan

first: Lourdes

last: Pena-Castillo

first: Sidharth

last: Chaudhry

first: Shaheynoor

last: Talukder

first: Benjamin

last: Blencowe

first: Quaid

middle: D

last: Morris

first: Timothy

last: Hughes

manufacture_protocol: Please refer to the manufacturer's web site at http://www.agilent.com/


title: Duke-GE/Amersham CodeLink UniSet Mouse 20K I Bioarray

city: Durham

first: Barry

last: Stripp

state: NC

address: 106 Research Drive, DUMC Box 103000

department: Medicine

institute: Duke University


title: 3.7k full genome LUMC BAC array, condensed version

city: Leiden

first: Marloes

last: van Kester

address: Einthovenweg 20

department: Dermatology

institute: Leiden University Medical Center

organism: Homo sapiens

description: This array represents a condensed version of GPL4012.

manufacture_protocol: The array contains 3700 probes spotted in triplicate on glass slides. The BAC set is distributed by the Welcome Trust Sanger Institute (Hinxton, UK), and comprises of 1 mb spaced probes, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. Reference: Knijnenburg J, Szuhai K, et.al. Am J Med Genet A. 2005 Jan 1;132(1):36-40. Insights from genomic microarrays into structural chromosome rearrangements.


title: Agilent Custom Tomato Gene Expression 4x44k Array AMADID: 19003

status: Public on Jun 05 2009

city: Rehovot

first: Imri

last: Ben-Israel

address: P.O box 12

department: Institute of Plant Sciences and Genetics in Agriculture

country: Israel

institute: Hebrew University

organism: Solanum lycopersicum

manufacture_protocol: Refer Manufactureres Website : www.agilent.com


title: [Mm35b_P05R] Affymetrix Mouse Tiling 2.0R Set, Array 5

status: Public on Feb 01 2008

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
Tiling array submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® Mouse Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the mouse genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.
Sequences used in the design of the Mouse Tiling 2.0R Array Set were selected from NCBI mouse genome assembly (Build 33). Repetitive elements were removed by RepeatMasker. The Mouse Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900852), or individual arrays from the set may be purchased separately.
Probes are tiled at an average resolution of 35 base pairs, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: See manufacturer's web site


title: [Mm35b_P06R] Affymetrix Mouse Tiling 2.0R Set, Array 6


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

status: Public on Mar 03 2008

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=Mon Mar 16 20:01:52 2009 PDT
#%chip_type=RaEx-1_0-st-v1
#%lib_set_name=RaEx-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


title: [Mm35b_P01R] Affymetrix Mouse Tiling 2.0R Set, Array 1


title: Indiana University Onthophagus taurus 3.5K cDNA microarray version 1

status: Public on Jun 01 2009

city: Bloomington

first: Justen

last: Andrews

state: IN

address: 915 East Third Street

department: Biology

institute: Indiana University

organism: Onthophagus taurus

manufacturer: The Center for Genomics and Bioinformatics, Indiana University

first: Teiya

last: Kijimoto

first: Armin

last: Moczek

first: Jade

last: Buchanan-Carter

first: Zach

last: Smith

first: Heejung

last: Yang

first: John

last: Colborne

first: Zhao

last: Lai

manufacture_protocol: We mainly followed the protocol of Indiana University Drosophila Genomics Resource Center (Andrews et al. 2006, http://cgb.indiana.edu/publications/alias/dgrc1_prod_protocol/version/current) to print microarrays with a minor revision of post-print wash.  Cleaned clones were dried completely, re-dissolved with DGRC spotting solution (1.5M Betaine in 3xSSC), and spotted on GAPSII MIcroarray Slides (Corning).  By using OmniGrid 300 printing robot, we printed 100 microarrays.  Followed by heating the spotted microarrays at 85°C for 3hrs, we rinsed them with 5xSSC/0.1%SDS (55°C), water (room temperature) twice, hot water (95°C), and another room temperature water then centrifuged them to dry.


title: [Dm35b_MR] Affymetrix Drosophila Tiling 1.0R Array

status: Public on Sep 21 2007

organism: Drosophila melanogaster

description:
Tiling array submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

This is the first generation of the Drosophila 1.0R Tiling Arrays. The Drosophila Tiling 1.0R Array uses 25-mer oligonucleotide probes, spaced evenly across the Drosophila genome at intervals of approximately 35 base pairs as measured from the center of a probe to the center position of the adjacent probe. Repetitive sequences were eliminated from the design using RepeatMasker software.

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: see manufacturer's web site


title: [Mm35b_P07R] Affymetrix Mouse Tiling 2.0R Set, Array 7


title: [Mm35b_P03R] Affymetrix Mouse Tiling 2.0R Set, Array 3


title: PIQOR (TM) Custom_CTID88 Microarray, mouse (88)

status: Public on Dec 31 2007

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

description: The PIQOR Custom_CTID88 Microarray comprises 792 immune related mouse specific cDNAs and 27 rat specific cDNAs. The 792 mouse cDNAs include 6 house-keeping genes as positive controls. Additional positive controls are given by 4 E. coli cDNA fragments, the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. 2 negative controls are given by spotted herring sperm DNA and buffer.Spotting in quadruplicate results in 3300 spots.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: [Hs35b_P05R] Affymetrix Human Tiling 2.0R Set, Array 5

status: Public on Mar 29 2007

description:
Tiling array submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® Human Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the human genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.
Sequences used in the design of the Human Tiling 2.0R Array Set were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. The Human Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900772), or individual arrays from the set may be purchased separately. The GeneChip® Human Promoter 1.0R Array is a subset of the Human Tiling 2.0R Tiling Array Set, and the content was chosen specifically to analyze protein/DNA interactions within promoter regions.
Probes are tiled at an average resolution of 35 base pair, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

BPMAP and other files can be downloaded from the Affymetrix Web site below.


title: [Hs35b_P02R] Affymetrix Human Tiling 2.0R Set, Array 2


title: [Hs35b_P04R] Affymetrix Human Tiling 2.0R Set, Array 4


title: [Hs35b_P07R] Affymetrix Human Tiling 2.0R Set, Array 7


title: [Hs35b_P03R] Affymetrix Human Tiling 2.0R Set, Array 3


title: [Hs35b_P06R] Affymetrix Human Tiling 2.0R Set, Array 6


title: [Sugar_Cane] Affymetrix Sugar Cane Genome Array

status: Public on Jun 09 2006

organism: Saccharum officinarum

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip Sugar Cane Genome Array contains 8,236 S. officinarum probe sets to monitor gene expression for approximately 6,024 distinct S. officinarum genes (including both UniGene and non-UniGene gene clusters).
The sequence information for this array was created in collaboration with leading sugar cane researchers through the GeneChip® Consortia Program and was designed based on content from Saccharum officinarum UniGene Build 5 from August 27th, 2004 and GenBank® mRNAs up to November 2, 2004. The array contains 11 probe pairs per probe set and is a 169-format, 11-micron array design.


title: [Mapping10K_Xba131] Affymetrix Human Mapping 10K SNP Array

status: Public on May 28 2004

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® Human Mapping 10K Array enables genotyping of greater than 10,000 Single Nucleotide Polymorphism (SNP) loci on a single array. The SNPs on this array were chosen from The SNP Consortium (TSC) database based on their presence on 250- to 1,000-basepair Xba I fragments in the human genome. SNPs were chosen based upon high reproducibility, call rate, accuracy, and physical map position. These SNPs have been validated across a minimum of 200 individuals from at least three distinct populations, Caucasian, Asian, and African-American. The average heterozygosity of the markers is greater than .35 across these populations.

Annotations taken from CSV (2.8 MB, 3/11/05).


title: [Medicago] Affymetrix Medicago Genome Array

status: Public on Dec 08 2006

organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip Medicago Genome Array is designed specifically to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. The Medicago Genome Array is particularly useful for agriculture researchers studying legume genomics and symbiotic relationships between nitrogen fixing bacteria and plants.
Sequence information for this array was selected from data sources including the TIGR M. truncatula gene index (The Institute for Genomic Research, January 2005), gene predictions from the International Medicago Genome Annotation Group (IMGAG), gene predictions from the S. meliloti genome, and M. sativa EST information made available by TIGR. The array contains over 61,200 probe sets: 32,167 M. truncatula EST/mRNA-based and chloroplast gene-based probe sets; 18,733 M. truncatula IMGAG and phase 2/3 BAC prediction-based probe sets; 1,896 M. sativa EST/mRNA-based probe sets; and 8,305 S. meliloti gene prediction-based probe sets.


title: [Mu19KsubB] Affymetrix Murine 19K SubB Array

status: Public on Mar 11 2002

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

Has 21146 entries and was indexed 29-Jan-2002.
Keywords = high density oligonucleotide array


title: [Mu19KsubA] Affymetrix Murine 19K SubA Array


title: [Citrus] Affymetrix Citrus Genome Array

status: Public on Aug 09 2007

organism: Citrus sinensis

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The array contains 30,171 probe sets representing up to 33,879 Citrus transcripts based on EST sequences obtained from several Citrus species and Citrus hybrids.

The array includes 46 probe sets representing several Citrus pathogens, and 60 probe sets representing various reporters, selectable markers, and transgenes. Also included are sequences from Poncirus and Poncirus crosses with Citrus hybrids.


title: [Maize] Affymetrix Maize Genome Array

status: Public on Jul 25 2006

organism: Zea mays

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip Maize Genome Array provides comprehensive coverage of over 100 cultivars present in NCBI's UniGene data set, including the most highly represented strains: B73, Ohio43, W22, W23, W64A, and Black Mexican Sweet.
The Maize Genome Array has 17,555 probe sets to interrogate approximately 14,850 Zea mays transcripts, which represent 13,339 genes (12,113 of which are represented in distinct UniGene clusters).
The sequence information for this array was selected from NCBI's GenBank® (up to September 29, 2004) and Zea mays UniGene Build 42 (July 23, 2004) databases. Probe sets on the array include 15 oligonucleotide pairs to detect each transcript, for added robustness and to facilitate detection of polymorphisms.


title: [Mu19KsubC] Affymetrix Murine 19K SubC Array


title: [Mapping10K_Xba142] Affymetrix Human Mapping 10K 2.0 Array

status: Public on Jul 18 2005

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

As with the previous-generation GeneChip® Mapping 10K Array, the GeneChip Mapping 10K 2.0 Array enables researchers to genotype more than 10,000 SNPs in a single experiment with one primer. The GeneChip Mapping 10K 2.0 Array contains equivalent content and performance as the original GeneChip Mapping 10K Array, but advances in photolithographic technology enable it to be produced in a smaller, more cost-efficient format. Now, researchers can genotype 10,000 SNPs in a single experiment at a cost comparable to microsatellite research.

Annotations derived from Affymetrix CSV file dated 6/21/2005.


title: [Bsubtilis] Affymetrix Bsubtilis Genome Array

status: Public on Jun 23 2003

organism: Bacillus subtilis

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

5021 entries and was indexed 30-Apr-2003


title: Mouse Genome 430 2.0 Array [Mm430_Mm_REFSEQ (v10) CDF]

city: Zurich

first: Francois

last: Verrey

address: Winterthurerstr. 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

organism: Mus musculus

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. Custom chip definition files (CDF) based on REFSEQ v10 (Brainarray) rather than Affymetrix annotation (Dai et al., PMID: 16284200).


title: Agilent-015957

status: Public on Sep 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

organism: Neisseria gonorrhoeae

first: Mollenkopf

last: Hans-Joachim

first: Friedrich

last: Alexandra

manufacture_protocol: 'in situ' SurePrint technology


title: [HG_U95E] Affymetrix Human Genome U95E Array

country: USA

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95).
Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent approximately 50,000 EST clusters.

Keywords = high density oligonucleotide array


title: [RAE230B] Affymetrix Rat Expression 230B Array

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

Array B of GeneChip Rat Expression Set 230
Has 15333 entries and was indexed 09-Apr-2003
Sequences used in the design of the array were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 99 of UniGene (June 2002) and refined by analysis and comparison with a number of other publicly available databases including the Baylor College of Medicine Human Genome Sequencing Center's preliminary rat genome assembly (June 2002). In addition, sequences were analyzed for untrimmed low-quality sequence information, correct orientation, false clustering, alternative splicing and alternative polyadenylation.