title: MMP_proteomic_qualitative

status: Public on Sep 20 2005

city: Seattle

first: Murray

last: Hackett

state: WA

address: HSB H330 1959 NE Pacific Street

department: Chemical Engineering

country: USA

institute: University of Washington

organism: Methanococcus maripaludis

technology: MS

description: Methanococcus maripaludis qualitative proteomics using ion trap mass spectrometry. Covers 1289 of 1722 predicted ORFs.

distribution: virtual

first: Yi

last: Zhang

first: Tiansong

last: Wang

first: Qiangwei

last: Xia


title: PSU_IntergenicYeast_V3,4

status: Public on Sep 21 2005

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

description:
PCR amplified yeast intergenic chip with ResGen Primer Pairs; Amplification as described at http://cmgm.stanford.edu/pbrown/protocols/2_DNA.html
Printed on aminosaline glass slides by the Penn State University Microarray facility
Keywords = spotted Yeast intergenic

distribution: non-commercial

first: Sara

middle: J

last: Zanton


title: P. gingivalis cKGM/KGM proteomics study

status: Public on Sep 17 2005

organism: Porphyromonas gingivalis

description: This set includes 977 P. gingivalis proteins identified in this study

first: Weibin

last: Chen

first: Ozlem

last: Yilmaz

first: Yoonsuk

last: Park

first: Il-Young

last: Jung

first: Richard

last: Lamont


title: GF100 GeneFilters

status: Public on Sep 24 2005

city: Kanazawa

first: Hiroshi

last: Sakurai

state: Ishikawa

address: 5-11-80 Kodatsuno

department: School of Health Sciences

country: Japan

institute: Kanazawa University

distribution: custom-commercial

manufacture_protocol: gene array


title: UCSF_mouse_900_v1.0

status: Public on Sep 13 2005

city: San Francisco

first: Graeme

last: Hodgson

state: CA

department: Neurological Surgery

institute: UCSF

organism: Mus musculus

first: John

middle: G

first: Joe

middle: W

last: Gray

first: Donna

last: Albertson

first: Daniel

last: Pinkel

first: Norma

last: Nowak

manufacture_protocol: Hodgson G, Hager JH, Volik S, Hariono S, Wernick M, Moore D, Nowak N, Albertson DG, Pinkel D, Collins C, Hanahan D, Gray JW. (2001) Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat Genet, 29, 459-64.


title: Agilent Human 1 cDNA Microarray (G4100A) [layout B]

status: Public on Jan 02 2004

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Homo sapiens

description:
12,814 unique clones, 97% map to named human genes
Sourced from Incyte's UniGene 1 and Human Drug Target DNA clone sets
Barcode location:Bottom
Scan Side:Front

This platform should be used for the following prints:

000478_D_20020807_FSPortraitBcodeDown
000478_D_20030121_FSPortraitBcodeDown
000526_D_20030121_FSPortraitBcodeDown
000478_D_20011130_FSPortraitBcodeDown

Please reference this platform if you used an array with the same layout, even if the print lot is different than specified above. The GEO staff will update the description of this platform to include additional print lots as encountered.

Print-specific information should be accounted for in the sample hybridization tables (eg. NULL value insertions for spots to be ignored).

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: MMP_proteomic_quantitative

first: Murray

last: Hackett

organism: Methanococcus maripaludis S2

description: Methanococcus maripaludis quantitative proteomics using isotope-labeling mass spectrometry. Covers 939 of 1722 predicted ORFs.


status: Public on Nov 13 2003

first: Terrill

middle: K.

last: McClanahan

address: 901 California Avenue

department: Experimental Pathology & Pharmacology

institute: DNAX Research Inc.

description: Incyte Gene Album Arrays 1-6 - public clones only.

first: Theodore

middle: R

last: Sana

first: Mary

last: Janatpour

first: Manjiri

last: Sathe

first: Leslie

middle: M

last: McEvoy

middle: K


title: CEA Yeast 7K Intergenic Microarray

status: Public on Sep 27 2005

city: Gif Sur Yvette

first: Michel

last: Werner

department: Biologie Joliot-Curie

country: France

institute: Commissariat à L'Energie Atomique-Saclay

description:
-Platform: amino-silane coated glass slides (GAPS II, Corning)

-S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic).

-The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)

first: Pascal

last: Soularue

first: Xavier

last: Gidrol

manufacture_protocol: See Description


title: Bauer Center for Genomics Research Caulobacter crescentus 50mer array

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

organism: Caulobacter vibrioides

technology: spotted oligonucleotide

manufacture_protocol: custom


title: Methanococcus maripaludis PCR-array

last: Leigh

department: Microbiology

description:
Methanococcus maripaludis array based on partial genome sequence. Covers 1597 of 1722 predicted orfs. PCR products spotted in duplicate on glass slides. Average length 500 bp.
Keywords: archaea, methanogen, anaerobic
Platform accession ID: NC_005791

first: Erik

last: Hendrickson


title: Infection and inflammation array

city: Boston

first: Nina

last: Reiniger

address: 181 Longwood Ave

department: Medicine

institute: Brigham & Women's Hospital, Channing Laboratory

description: cDNA spotted array. 4608 spots representing genes, ESTs and controls. Some genes were selected for their involvement in response to infection and inflammation.


title: UCSF_mouse_1344_v1.1

first: Graeme

last: Hodgson

first: John

last: Gray


title: UCSF_mouse_1056_v1.0

first: Joe


title: UCSF_mouse_1344_v1.0


title: UCSF_mouse_288_v1.0


title: yeast_nucleosome_positioning_microarray 10+

status: Public on Sep 01 2005

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description:
The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 223 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.
Note:  this platform does not contain any control oligonucleotides.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microarray

manufacturer: Brown Lab, Biochemistry Dept., Stanford University

manufacture_protocol: MGuide, www.microarrays.org


title: Tiling design for D. melanogaster

status: Public on Sep 11 2005

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Drosophila melanogaster

technology: in situ oligonucleotide

description: All of Chr 4, 2L, pericentric regions on 2, first 2MB on X and part of 2R. Based on FlyBase release 3.2.2. One 60mer per 100 bases.

first: Steven

first: Bas

last: van Steensel


title: BDGP microarray

city: Tucson

first: Therese

middle: Ann

last: Markow

state: AZ

address: 310 Biosciences West

department: EEB

institute: University of Arizona

description:
These cDNA microarrays were printed by the Genetic Analysis and Technology Core Custom Microarray Facility at the University of Arizona.
Printing material was amplified from BDGP Unigene library v1.0 containing 6K ESTs.

These arrays were used to assess differential gene expression between larvae reared on a cornmeal medium diet, and larvae switched to a pure banana diet.
Keywords = dietary shifts
Keywords = functional genomics

first: Laura

middle: D

last: Carsten

first: Tom

last: Watts

middle: A


title: Meyerowitz Lab Arabidopsis Operon Array Version 3

status: Public on Sep 07 2005

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

organism: Arabidopsis thaliana

description: This microarray is based on the Arabidopsis Genome Oligo Set Version 1.0 and on the Arabidopsis Genome Oligo Set Version 1.0 Upgrade (Operon, Alameda, CA). These sets consist of a total of 30,194 oligonucleotides that correspond to 26,753 annotated Arabidopsis genes.

manufacturer: Meyerowitz Laboratory at the California Institute of Technology

first: JoseLuis

last: Riechmann

first: Elliot

last: Meyerowitz

manufacture_protocol: The oligonucleotides of the Arabidopsis Genome Oligo Set (Operon) were provided in 384-well plates. The dried DNA was resuspended in 15 ul of printing buffer (150 mM Na-phosphate pH 8.5) per well, resulting in an estimated DNA concentration of 40 uM. DNA was spotted onto poly-lysine coated glass slides with a MicroGrid II spotter (Biorobotics) using Microspot 10K quill pins (Biorobotics). After printing, the slides were processed and blocked following standard protocols.


title: Ramaciotti 15k mouse slides

city: Sydney

first: Peter

last: Little

country: Australia

institute: School of Biotechnology and Biomolecular Sciences, The University of New South Wales

manufacturer: Ramaciotti Centre for Gene Function Analysis

first: Chris

last: Cotsapas

middle: F

manufacture_protocol:
This slide contains the NIA 15K cDNA clone set [1] and the Lucidea mouse ScoreCard [2], arrayed in 32 blocks on polyamine slides.

[1]  Kargul et al 2001, Nat. Genet. 28(1): 17-18
 [2] http://www5.amershambiosciences.com/aptrix/upp01077.nsf/Content/microarrays_control_reagents_universal_scorecard)


title: yeast_nucleosome_positioning_microarray 6-9

description:
The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 230 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.  This platform contains two extra plates compared to Platform GPL1950.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microarray

manufacturer: Center for Genomics Research, Harvard University


title: UI Human EST 37K cDNA array

status: Public on Sep 10 2005

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description:
Glass slide with 37,632 spots (34,462 unique cDNA clone inserts) in 48 blocks consisting of 28 columns and 28 rows.  Blocks are arranged in 12 rows and 4 columns.
The set of 34,462 cDNA clone inserts was identified from the University of Iowa EST collection.  The clone inserts were amplified with T7 and T3 primers and printed with 50% DMSO on UltraGaps slides (Corning) using a ProSys 5510 Microarray Printer
A small set of full-length clones were ordered from the IMAGE Consortium and spotted on the array.

first: Irina

middle: V

last: Koroleva

first: Einat

last: Snir

first: Hakeem

last: Almabrazi

first: Thomas

middle: L

last: Casavant

first: Marcello

middle: B

last: Soares

manufacture_protocol: The clone inserts were amplified directly from bacterial cell cultures with T7 and T3 primers, purified, dried, resuspended in water and printed with 50% DMSO on UltraGaps slides (Corning) using a ProSys 5510 Microarray Printer.  The 16 control spikes were printed by each pin, at the beginning or at the end of the pin printing area.  The spotted slides were cross-linked and stored in a desiccator.


title: WUSTL Brugia malayi v.1

status: Public on Dec 06 2004

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

organism: Brugia malayi

description:
B. malayi clusters for arrays were selected from 8392 clusters generated and posted at the website http://nema.cap.ed.ac.uk/nematodeESTs/nembase
These clusters were derived from > 20 cDNA libraries that represent the major B. malayi life cycle stages.  They represent approximately ~40% of the total number of predicted genes for B. malayi.
Clusters with multiple ESTs, predicted homology by BLAST, and sequence permitting design of a unique 65-mer oligonucleotides were chosen for inclusion on the array.  Oligos were synthesized from the consensus sequence of selected clusters (n=3569) by standard methods by Illumina (San Diego, CA).   The oligonucleotides (50nM in 3x SSC with 0.75M betaine) were printed in duplicate on MWG Epoxy slides (MWG Biotech Inc, High point, NC) by a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/ ).
Keywords = brugia malayi nematode worm parasite filaria filariasis

first: Ben

last: Li

first: Wes

last: Warren

last: Williams

first: Gary

last: Weil

first: Amy

middle: C

last: Rush