title: HUMAN_21K_OligoArray_1

status: Public on Feb 18 2004

city: San Antonio

first: Phillip

last: Bowman

state: TX

address: 3400 Rawley E. Chambers Ave

country: USA

institute: Institute of Surgical Research

organism: Homo sapiens

technology: spotted oligonucleotide

description:
Spotted 70mer oligonucleotide.
The Human Array Ready Oligo Set Version 2 contains arrayable 70mers representing 21,329 well-characterized human genes from the UniGene Database. This database is located at the National Center for Biotechnology Information (see www.ncbi.nlm.nih.gov/UniGene/). All 70mer oligonucleotides in the Human Genome Oligo Set Version 2 were designed after the representative sequences in the UniGene Database, Build Hs 147.
The 70mers have also been Tm normalized to 78°C (±5 C). The Tm normalization allows for a more stringent hybridization at higher temperatures.  When a 70-mer could not be designed within the specified Tm range, a shorter or longer length oligo was substituted to maintain the stringent Tm conditions. There are also 12 positive controls and 12 negative controls provided in 16 replicates.
Keywords = spotted
Keywords = 70mer oligonucleotide

distribution: non-commercial

middle: D

first: Baiteng

last: Zhao


title: Mouse oligo array sigmagenosys oligolibrary

status: Public on Apr 01 2006

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Mus musculus

description:
Mouse OligoLibrary by SigmaGenosys, 384 well format, 58 plates, replicate spotted in 4x12 subgrids, each 31x31 spots
Keywords = oligoarray
Keywords = oligolibrary
Keywords = mouse

first: Chris

first: Bettina

last: Harr

first: Diethard

last: Tautz


title: NKI/CMF Human 18k cDNA spotted microarray

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

technology: spotted DNA/cDNA

description: Spotted cDNA microarray containing 19200 spots: 768 control/empty spots and 18432 cDNA clones, selected from the Research Genetics Human Sequence Verified library. Clones were selected based on the availability of annotation data.

manufacturer: Central Microarray Facility at the Netherlands Cancer Institute

first: Annuska

middle: M

last: Glas

first: Daphne

last: de Jong

first: Ed

last: Schuuring

first: Philip

last: Kluin

manufacture_protocol: See CMF website: http://microarray.nki.nl/download/protocols_o.html


title: GE Healthcare/Amersham Biosciences CodeLink™   UniSet Rat I Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

organism: Rattus norvegicus

description:
CodeLink UniSet Rat I is designed for expression monitoring of a broad range of rat genes derived from NCBI and clustered to generate consensus sequences. Identifying patterns of differential mRNA expression over a large set of genes is an excellent method to identify targets, characterize action mechanisms, and make initial predictions of global drug effects. Well-annotated mRNA or coding sequences were chosen from the entire UniGene set to ensure usefulness to a large range of researchers in basic research, biotechnology, and drug development applications. Each sequence was carefully screened to reduce gene redundancy and to design high-quality specific probes.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.

distribution: commercial


title: Bacillus subtilis WDG16 platform

status: Public on Apr 15 2006

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

organism: Bacillus subtilis

first: Richard

last: Losick

first: Jenny

last: Auchtung

first: Tommy

first: Robert

last: Britton

first: Elke

last: Kuester-Schoeck

manufacture_protocol:
Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD.Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
J Bacteriol. 2002 Sep;184(17):4881-90.


title: Bacillus subtilis WDG13 platform

manufacture_protocol:
Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
J Bacteriol. 2002 Sep;184(17):4881-90.


title: Bacillus subtilis whole genome array print 8

first: Jennifer

first: Catherine

middle: A

last: Lee

first: Rob

first: Natalia

last: Comella

first: Emily

last: Ruiz

first: Thomas

manufacture_protocol: DNA amplified from Bacillus subtilis strain JH642 chromosomal DNA using ORFmer primer set from Sigmagenosys as well as additional oligos.  PCR products were purified, lyophilized, and resuspended in 50% DMSO.  Products were spotted on to Corning GAPS II slides.


title: Ontario Cancer Institute Mus musculus 31K cDNA microarrays

status: Public on Apr 12 2006

city: Oak Ridge

first: Yesim

last: Aydin Son

state: TN

address: ORNL, Bethel Valley Road, Building 1061,MS-6445

department: Functional Genomics Group

institute: UT-ORNL Graduate School of Genome Science and Technology

manufacturer: Microarray Centre at UHN, Toronto, Ontario

manufacture_protocol: NIA/NIH 15K mouse cDNA clone set printed in duplicates on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use.


title: FHCRC Arabidopsis Oligo Array v1.0

status: Public on Mar 18 2005

city: Seattle

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

organism: Arabidopsis thaliana

description: Operon Arabidopsis Genome Oligo Set Version 1.0 containing 26,090 70mer probes representing 26,029 Arabidopsis thaliana genes.  The  26,090 probes were designed from experimentally determined or cloned genes, expressed sequence tag (EST) sequences, and predicted transcripts.  A majority of the probes (26,086) were designed from the  UniGene Database Build At 4 developed and maintained at the National Center of Biotechnology Information (NCBI).  The other 4 probes were designed from GenBank sequences not in the UniGene Build At 4.


title: NMDA-induced genes

status: Public on Apr 26 2006

city: Baltimore

first: Ted

last: Dawson

state: MD

address: 733 N. Broadway, MRB SUITE 731

department: Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

description: Rat cDNA filter of NMDA-induced genes, previously screened from rat cortical neurons after NMDA treatment

first: Suk

middle: J

last: Hong

first: Jean-François

last: Haince

first: Sunghee

last: Cho

first: Costantino

last: Iadecola

first: Guy

middle: G

last: Poirier

first: Valina

middle: L


title: Affymetrix GeneChip Arabidopsis 8k

status: Public on Sep 04 2005

city: Capital Federal

first: Maria

middle: Agustina

last: Mazzella

state: Buenos AIres

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI

technology: in situ oligonucleotide

manufacture_protocol: See manufacture´s web site


title: CNIO H. sapiens 26.7k Oncochip 2

status: Public on Apr 07 2006

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: Oncochip 2


title: Dichelobacter nodosus oligonucleotide microarray

status: Public on Apr 17 2006

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

organism: Dichelobacter nodosus

description: Microarrays consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation) spotted in triplicate on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org) and where possible two gene probes per ORF were synthesised.  Oligonucleotides were spotted on a 2X6 metagrid, which was composed of 24X26 subgrids.

first: Dane

last: Parker

first: Ruth

last: Kennan

first: Gary

middle: S

last: Myers

first: Ian

middle: T

last: Paulsen

manufacture_protocol: Microarrays were constructed in house and consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation; Gary Myers and Ian Paulsen, TIGR) spotted in triplicate with 50% DMSO on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs, as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org).


title: Compugen Zebrafish 16K

status: Public on Apr 30 2006

city: Brisbane

first: Karin

middle: Sonja

last: Kassahn

state: QLD

address: Queensland Bioscience Precinct

department: Institute for Molecular Bioscience

institute: University of Queensland

organism: Danio rerio

first: Alister

middle: C

last: Ward

manufacture_protocol: Spotted oligonucleotide array, 65mers based on Compugen 16K Danio rerio OligoLibrary XEBLIB96 version 2.1, includes various controls


title: Sookmyung Mouse 10K (EScell)

status: Public on Apr 18 2006

city: Seoul

first: Young Ju

last: Suh

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

last: Shim

last: Yang

last: Park

manufacture_protocol: spotted cDNA on glass slide


title: ORNL-CAG mouse 15k array

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

first: Brynn

last: Voy

manufacture_protocol:
Please refer to the below:
Hu, R., Hebbar, V., Kim, B-R., Chen, C., Winnik, B., Buckley, B., Soteropoulos, P., Tolias, P., Hart, R.P, and Kong, A-N.T. (2004) In vivo pharmacokinetics and pegulation of gene expression profiles by isothiocyanate sulforaphane in the rat. J. Pharmacol. Exp. Ther. 310, 263-71.


title: Bacillus subtilis bso6 platform

first: Alan

last: Grossman

first: Robert

last: Britton

first: Elke

last: Kuester-Shoeck

first: Jenny

last: Auchtung

first: Catherine

last: Lee

manufacture_protocol:
Auchtung et al. Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response.
Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12554-9.

65mer oligo library purchased from Sigma


title: CNIO H. sapiens 13.6k Oncochip 1

last: Hernandez-Vargas

description: Oncochip 1


title: WTSI Xenopus tropicalis 2.5K array v2.1.1

status: Public on Apr 13 2006

city: Hinxton

first: Matthew

last: Clark

address: Wellcome Trust Genome Campus

department: Vertebrate Geneitcs and Development

country: United Kingdom

institute: Wellcome Trust Sanger Institute

organism: Xenopus tropicalis

description: GE Healthcare Codelink

first: Mario

last: Caccamo

first: Derek

last: Stemple

manufacture_protocol: Spotted 5prime amino linked 65mers (Illumina) @50nM with a BioRobotics MicroGrid II Pro onto GE Healthcare Codelink slides according to manufacturer's instuctions.


title: NKI-CMF Homo sapiens 19k cDNA array

city: Amsterdam

first: Daoud

last: Sie

address: Plesmanlaan 161

institute: Dutch Cancer Institute

description: Glass coating: Poly-L-Lysine

manufacturer: Central Microarray Facility, NKI Amsterdam

first: W

last: Brugman

first: M

last: Heimerikx

first: D

first: A

last: Velds

last: Nieuwland

first: R

last: Kerkhoven

manufacture_protocol:
The human cDNA arrays we print contain a part of the sequence verified Invitrogen cDNA library of 45K. We selected the genes that are named as well as added a collection of ESTs to print on the array.
This means that approximately 11000 sequences belong to named genes of which around 7000 are unique. The arrays consist of 19600 features printed in a 20x20 subarray layout using 48 Biorobotic 2500-microspot pins and are commonly referred to as our 18K human cDNA arrays. We are printing purified PCR products that vary in length from 200 to 4000 bp. All PCRs have been checked on gel.


title: Bacillus subtilis WDG12 platform


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv304.03.Z)

status: Public on Apr 27 2006

city: Tucson

first: David

middle: William

last: Galbraith

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

manufacturer: The Galbraith Laboratory, University of Arizona

middle: W

manufacture_protocol: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv304.03.001-ATv304.03.300 (http://www.ag.arizona.edu/microarray).


title: amersham mouse 20k

status: Public on Apr 22 2006

city: La Jolla

first: Tomokatsu

last: Ikawa

state: CA

address: 9500 Gilman Drive

institute: UCSD

distribution: custom-commercial


title: RIKILT mouse oligo 10K array

city: Wageningen

first: ping

last: wang

address: bornsesteeg 45

institute: RIKILT / Maastricht University

first: Ping

last: Wang

first: Annelies

last: Bunschoten

first: Yvonne

last: Dommels

first: Edwin

last: Mariman

first: Jaap

last: Keijer

manufacture_protocol: The 10K MWG mouse oligoset (10K_A, MWG-Biotech AG, Ebersberg, Germany) together with additional 50-mer oligo probes genes encoding secretory proteins and proteins involved in energy metabolism, were in-house printed on GAP II coated slides (Corning), using the Microgrid II arrayer (BioRobotics Ltd, Cambridge, UK). Majority of the probes of the additional oligoset of the extra set were also from MWG. The rest (8 genes) were designed through OligoFaktory server (http://ueg.ulb.ac.be/oligofaktory/index.jsp) and synthesized by Isogen (Maarssen, the Netherlands) and Biolegio (Nijmegen, the Netherlands). After printing, microarrays were allowed to dry at room temperature. The oligo arrays were immobilized by UV cross-linking (120 MJ of UV energy). The microarray slides were then prewashed in the following order to reduce background; 20 minutes at 55C with 2x SSC/0.2% SDS, 5 minutes at room temperature (RT) with 0.2x SSC and 3 minutes at RT with demineralized water. Slides were dried by 2 minutes of centrifugation (2000 rpm).


title: Bacillus subtilis WGD14 platform

first: Alan

last: Grossman

first: Robert

last: Britton

first: Elke

last: Kuester-Shoeck

first: Tommy

last: Auchtung

first: Jenny

first: P.

last: Fawcett

last: Eichenberger

first: Richard

last: Losick

first: J.

middle: E

last: Gonzales-Pastor

manufacture_protocol:
Please read Britton et al. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
J Bacteriol. 2002 Sep;184(17):4881-90.


title: Bacillus subtilis oligonucleotide array print #2

first: Jennifer

first: Catherine

last: Lee

middle: D

first: Rob

last: Kuester-Schoeck

manufacture_protocol: Resuspended portion of B. subtilis OligoLibrary from SigmaGenosys, catalog number BACLIB96, to 25 micromolar in 50% DMSO. These oligonucleotides are 65 nt in length and correspond to the 4106 annotated genes present in Subtilist genome data release R16.1. Oligos were spotted on to Corning UltraGAPS slides.


title: Tor Vergata Mus musculus 200 22q11Ds chip

status: Public on Apr 11 2006

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

first: Michela

last: Biancolella

first: Daniela

last: Minella

first: Giuseppe

last: Novelli

manufacture_protocol:
Each oligonucleotide probe was diluited in a spotting buffer (Corning, Schiphol-rijk, The Netherlands) at a final concentration of 50 pmoli/ul. After this, oliigonucleotide probes were mechanically “spotted” onto UltraGAPS glass slides (Corning, Schiphol-rijk, The Netherlands) using The RoboArrayer™ (Microgrid Compact Plus, BioRobotics ).
Each oligonucleotide probe was represented in triplicate per array. Printing conditions were humidity among 50-55% and temperature 25°C. Printed slides were dried overnight and cross-linked with UV light at 600 mJ using a Strata-linker 2400 (Stratagene, Glenville, VA) and stored in a desiccator at room temperature.


title: Maize CornChip0 8.5K GeneChip

status: Public on Apr 14 2006

city: Ames

first: Roger

last: Wise

state: IA

address: 411 Bessey Hall

institute: Iowa State University

organism: Zea mays

description: The Maize CornChip0 comprises 8,403 probesets, each represented by a set of 30 PM and 30 MM probes. Probe sets were designed from B73 (4,050) or from a contig consensus of mixed maize line DNA sequences (4,353), and were based on EST singletons (2,811), EST clusters (4,295) and other non-EST derived cDNA sequences (1,297).

middle: P

first: Virginia

last: Walbot

first: Gene

last: Tanimoto

manufacture_protocol: The Maize CornChip0 was manufactured using standard proprietary procedures from Affymetrix.


title: SIPPE Gossypium hirsutum 5K cDNA fiber and ovule array

city: Shanghai

first: Xiao-Ya

last: Chen

address: No. 300, Fenglin Road

country: China

organism: Gossypium hirsutum

description: To construct a cotton cDNA library, total RNA was isolated from the -3- to 3-DPA ovules and 6- to 24-DPA fibers by a cold-phenol method as previously described (Li, et al. 2002). Poly (A)+RNA was purified by an Oligotex mRNA Midi kit (QIAGEN, Valencia, CA) according to the manufacture’s instruction, and cDNA libraries were constructed following the ZAP-cDNA Synthesis kit (STRATAGENE，La Jolla, CA). The cDNA inserts were sequenced with T7 primer by ABI3700 automatic Sequencer. The ESTs have been deposited into NCBI database with accession number from DT_046365 to DT_054205.

manufacturer: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 20003, China

first: Jin-Ying

last: Gou

first: Ling-Jian

last: Wang

manufacture_protocol: Based on cluster and annotation, 5122 putative unique EST clones were selected and their inserts were amplified by PCR, using T3 and T7 primers. House-keeping histones (H2A, H2B, H3, and H4) were included as internal controls. After purification and quantification, the PCR products plotted onto the glass slides (Full Moon BioSystems, Sunnyvale, CA) by GeneMachines OmniGrid Microarrayer (BST Group，Singapore).  Probes were prepared by the MICROMAX TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA, USA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 C, and arrays were washed thrice for 20 min each: 60 C in 2×SSC/0.2SDS, room temperature in 2×SSC, and room temperature with 0.2×SSC.


title: UCSF_HumArray

city: San Francisco

first: Joan

last: Climent

address: 2340 Sutter St

department: Cancer Research Institute

institute: UCSF Cancer Center

first: Peter

last: Dimitrov

first: Jane

last: Fridlyand

first: Jose

last: Palacios

first: Reiner

last: Siebert

first: Donna

last: Albertson

first: Joe

last: Gray

first: Daniel

last: Pinkel

first: Ana

last: Lluch

last: Martinez-Climent


title: DNAChipConsortium_Rat_Ver1

city: Tokyo

first: Toshiaki

last: Monkawa

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Internal Medicine

country: Japan

institute: Keio University School of Medicine

manufacture_protocol: 60-65 mer oligonucleotides were spotted.


title: Tursiops truncatus cDNA Microarray version 1.0

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

organism: Tursiops truncatus

manufacturer: Hollings Marine Laboratory, Genomics Core

first: Annalaura

last: Mancia

first: Mats

last: Lundqvist

first: Sebastiano

last: Gattoni-Celli

manufacture_protocol: as described by Mancia et al. (in prep)


title: ISU Maize 12k cDNA Generation II Version B.1-IG

first: Patrick

middle: S.

last: Schnable

address: 2035B Roy J Carver Co-Lab

manufacturer: Schnable Laboratory at Iowa State University

manufacture_protocol: The ISU microarray facility have generated a maize gene chip that contains 12,160 spotted cDNA inserts. These cDNA clones were obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable.


title: ENCODE NimbleGen hg16 tiling array

status: Public on Mar 09 2006

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

first: Shally

last: Xu

first: Peggy

last: Farnham

first: Michael

last: Singer

first: Roland

last: Green

manufacture_protocol: tiling array; see NimbleGen website. Note that one 50 mer every 38 nts. Repeats are not included in array.


title: Institute of Food Research Salmonella typhimurium LT2 5.8K array

status: Public on Apr 04 2006

city: Norwich

first: Arthur

last: Thompson

state: Norfolk

address: Colney Lane

department: Food Safety Science

institute: Institute of Food Research

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

first: Sacha

last: Lucchini

first: Jay

last: Hinton

manufacture_protocol: PCR product array of whole ORF's from S. Typhimurium LT2. For description of PCR amplification and printing procedures see Eriksson et al., Molecular Microbiology(2003) 47(1): 103-118.


title: Affymetrix custom microarray to profile mirna

status: Public on Mar 24 2006

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Stem Cell and Developmental Biology

country: Singapore

institute: Genome Institute of Singapore

description: This set includes 347 oligonucleotides, mostly 20-mers, designed to measure expression leveles of microRNA.

manufacture_protocol: as described in manufacturers website


title: Gene expression profiling of 19 cattle tissues reveals unique patterns related to tissue function

city: Urbana

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

organism: Bos taurus

description: TeleChem superamine slides

middle: R

first: Robin

last: Everts

first: Zonglin

last: Liu

first: Dawn

last: Morin

first: Jonathon

middle: U

last: Peled

first: Sandra

last: Rodriguez-Zas

first: Harris

last: Lewin

manufacture_protocol: Amplification of vector insert from bacterial subculture. Cleanup by Millipore filter. PCR product was printed in 3 x SSC + 1.5M Betaine.


title: LAFUGA Cattle subtr lib 18KB v1.0

status: Public on Dec 31 2005

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description:
Pretreatment of Animals and Collection of Endometrial Tissue Samples for the production of subtracted cDNA libraries:

Ten cyclic heifers (Deutsches Fleckvieh, Simmental) between 18 and 24 months old were cycle synchronized by injecting intramuscularly a single dose of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, Munich, Germany) at dioestrus. Animals were observed for sexual behaviour (i.e., toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate injection. In addition, animals were checked with ultrasound-guided follicle monitoring. Blood samples were taken at day 20, day 0 of the estrous cycle and just before slaughtering to determine serum progesterone (P4) levels. The first group of animals was inseminated with cryo-conserved sperm (ejaculate + diluter 1:10) at estrus. Animals were slaughtered at Day 18 of gestation and intact concepti were detected in the ipsilateral uterine horns of the animals used for gene expression analysis (n=4). Control animals (n=6) were inseminated with the supernatant of centrifuged sperm and also slaughtered at day 18 of the estrous cycle to achieve an identical as possible pretreatment of both groups. No conceptus was found in control animals. Sperm was derived from the same bull. The uterus was prepared and opened longitudinally. In pregnant animals, the conceptus was localized and carefully removed. Samples were carefully cut out from the lamina propria of the intercaruncular endometrium with a scalpel and immediately transferred into an appropriate amount of RNAlater (Ambion). Tissue sample of the caudal part of the ipsilateral uterine horn were used for transcriptome analyses.Samples were stored at -20°C until further processing.

Generation of Subtracted cDNA Libraries:
The production of subtracted libraries was done according to the Suppression Subtractive Hybridization (SSH) method (Diatchenko et al. 1996). Total RNA from endometrial tissue samples of the ipsilateral caudal part of the uterus was isolated using Trizol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's recommendations. The quantity and quality of total RNA was determined by spectrometry and agarose gel electrophoresis. Sixty microgram of pooled total RNA (corresponding to approximately 1.8 µg mRNA) were used for the preparation of subtracted cDNA libraries for pregnant and control animals, respectively. The construction of the libraries was done as previously described (Bauersachs S et al. 2003; Bauersachs S et al. 2004) with the modification that no additional driver cDNA was added at the second step of subtractive hybridization. For every library 1,536 cDNA clones were randomly picked. This array (LAFUGA Cattle subtr lib 18KB v1.0) contains the cDNA clones derived from the subtracted library (18KB) enriched for cDNAs of genes upregulated in endometrium of Day 18 pregnant animals.

manufacturer: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians University of Munich

manufacture_protocol: 1,536 cDNA clones were randomly picked for each library and grown overnight at 37 °C in 100 µl LB medium in 96-well microtiter plates. Bacterial suspensions were diluted 20-fold in TE buffer (pH 8.0), incubated at 96 °C for 10 min, and stored at -20 °C. PCR amplification of the cDNA insertions was performed in 20 µl in 96-well cycle plates and contained 1 µl diluted bacterial cells, PCR buffer (peQLab, Erlangen, Germany), 200 pmol/µl dNTPs, 0.3 pmol/µl of the respective primers (modified T3 and T7 primers), and 1 U Taq DNA polymerase (peQLab). All PCR products were analysed by 0.8 % agarose gel electrophoresis showing that more than 95 % of the PCR reactions yielded defined PCR products. 15 µl of PCR reactions were transferred to 384-well microtiter plates (ABgene) containing 15 µl 2-fold spotting buffer (40 mmol/l Tris-HCl pH 8, 2 M NaCl, 2 mmol/l EDTA, bromophenol blue). 1,536 PCR products were spotted onto nylon membranes (Nytran Supercharge, Schleicher & Schuell, Dassel Germany) on an area of 20 x 50 mm using an Omnigrid Accent microarrayer (GeneMachines, San Carlos, California, USA) and solid pins (SSP015, diameter 0.015 inches; Telechem International, Sunnyvale, California, USA). Spotting was done 6 times for each PCR product on the same position for sufficient and equal application. 25 arrays were produced simultaneously. The cDNAs were denatured on the arrays by incubation on filter paper (Schleicher & Schuell) soaked with 0.5 N NaOH for 20 min at room temperature. DNA was fixed by baking at 80 °C for 30 min and UV cross-linking (120 mJ/cm2, XL-1500 UV Crosslinker, Spectronics Corp., New York, USA).


title: LAFUGA Cattle subtr lib 18KO v1.0

description:
Pretreatment of Animals and Collection of Endometrial Tissue Samples for the production of subtracted cDNA libraries:

Ten cyclic heifers (Deutsches Fleckvieh, Simmental) between 18 and 24 months old were cycle synchronized by injecting intramuscularly a single dose of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, Munich, Germany) at dioestrus. Animals were observed for sexual behaviour (i.e., toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate injection. In addition, animals were checked with ultrasound-guided follicle monitoring. Blood samples were taken at day 20, day 0 of the estrous cycle and just before slaughtering to determine serum progesterone (P4) levels. The first group of animals was inseminated with cryo-conserved sperm (ejaculate + diluter 1:10) at estrus. Animals were slaughtered at Day 18 of gestation and intact concepti were detected in the ipsilateral uterine horns of the animals used for gene expression analysis (n=4). Control animals (n=6) were inseminated with the supernatant of centrifuged sperm and also slaughtered at day 18 of the estrous cycle to achieve an identical as possible pretreatment of both groups. No conceptus was found in control animals. Sperm was derived from the same bull. The uterus was prepared and opened longitudinally. In pregnant animals, the conceptus was localized and carefully removed. Samples were carefully cut out from the lamina propria of the intercaruncular endometrium with a scalpel and immediately transferred into an appropriate amount of RNAlater (Ambion). Tissue sample of the caudal part of the ipsilateral uterine horn were used for transcriptome analyses.Samples were stored at -20°C until further processing.

Generation of Subtracted cDNA Libraries: The production of subtracted libraries was done according to the Suppression Subtractive Hybridization (SSH) method (Diatchenko et al. 1996). Total RNA from endometrial tissue samples of the ipsilateral caudal part of the uterus was isolated using Trizol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's recommendations. The quantity and quality of total RNA was determined by spectrometry and agarose gel electrophoresis. Sixty microgram of pooled total RNA (corresponding to approximately 1.8 µg mRNA) were used for the preparation of subtracted cDNA libraries for pregnant and control animals, respectively. The construction of the libraries was done as previously described (Bauersachs S et al. 2003; Bauersachs S et al. 2004) with the modification that no additional driver cDNA was added at the second step of subtractive hybridization. For every library 1,536 cDNA clones were randomly picked. This array (LAFUGA Cattle subtr lib 18KO v1.0) contains the cDNA clones derived from the subtracted library (18KO) enriched for cDNAs of genes downregulated in endometrium of Day 18 pregnant animals compared to non-pregnant controls.


title: GE Healthcare/Amersham Biosciences CodeLink™   UniSet Mouse 20K I Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

description:
CodeLink UniSet Mouse 20K I Bioarray content is based on the public NCBI, UniGene, and RefSeq databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. Every probe was functionally validated against multiple tissues to ensure best representation of the gene so that the results will be biologically relevant. Every bioarray is also functionally validated during production to further ensure quality performance.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.


title: GE Healthcare/Amersham Biosciences CodeLink™   ADME Rat 16-Assay Bioarray

description:
CodeLink ADME Rat 16-Assay Bioarrays are designed to deliver biologically relevant results for ADME and toxicology studies. Each bioarray contains 16 arrays—each with ~1280 single stranded oligonucleotide probes derived from publicly available, well annotated mRNA sequences found in the Rat UniGene set of unique clusters. Each sequence was carefully screened to reduce gene redundancy and design high-quality, specific probes. Every probe is functionally validated to ensure reliable performance for ADME and toxicological applications.

CodeLink ADME Rat 16-Assay Bioarray utilizes the multiassay bioarray format and is currently available as a catalog item.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.


title: GE Healthcare/Amersham Biosciences CodeLink™   UniSet Human I Bioarray

description:
~10 000 human genes (unique accession numbers)- one specific, prescreened 30-mer probe per gene,
functionally validated. One set of housekeeping genes that may be used for baseline normalization.
68 bacterial control probes. 18 positive control probes to monitor cDNA and cRNA synthesis and array
activity. 50 negative control probes to determine threshold and assess background.
Six positive control bacterial spikes included in cDNA Synthesis Kit.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.


title: B. subtilis_full genome_PCR_ver.5

status: Public on Sep 01 2004

city: Cambridge

first: Patrick

middle: Yves

last: Eichenberger

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

institute: Harvard University

description:
The arrays consist of PCR amplified products from 4,100 protein-coding genes corresponding to release 15.1 of the B. subtilis genome described at http://genolist.pasteur.fr/SubtiList/
Primers for PCR amplification were purchased from Sigma-Genosys.
Details of the PCR amplification and purification procedure can be found in Britton, R. A., Eichenberger, P., Gonzalez-Pastor, J. E., Fawcett, P., Monson, R., Losick, R. and Grossman A. D. (2002). Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J Bacteriol 184, 4881-4890.
PCR amplification was considered successful for 3,920 of the 4,100 template genes by electrophoresis of the PCR products on agarose gels. New primers were designed for 180 genes and 154 of these were successfully amplified. Therefore a total of 4,074 PCR products (>99% of the annotated protein-coding genes of B. subtilis) were spotted on the slides.
PCR products were dried down and resuspended in 3x SSC-0.1% Sarkosyl and spotted on CMT-GAPS slides (Corning) with the CGR arrayer described at http://www.cgr.harvard.edu/Resources/Instrumentation/instrumentation.html
The quality of each set of printed arrays was checked by hybridization of Cy3 or Cy5 labeled B. subtilis chromosomal DNA isolated from strain PY79.

first: Jose

last: Gonzalez-Pastor

first: Richard

last: Losick


title: GE Healthcare/Amersham Biosciences CodeLink™   UniSet Mouse I Bioarray

description:
CodeLink UniSet Mouse I Bioarray contains single-stranded oligonucleotide probes derived from a large majority of publicly available, well-annotated mRNA sequences found in the Mouse UniGene set of unique clusters. Each bioarray contains probes for an independent assay of all 10,000 genes in the set.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.


title: FG001 Genomic Tiling Array

status: Public on May 30 2005

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

organism: Drosophila melanogaster

description: Tiling array from selected regions of the Drosophila genome (adh-region and hsp genes) used in anti-HSF chromatin immunopurification experiments.

first: Steven

first: Robert

middle: A

last: White

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: David

last: Huen

last: McGirr