title: RAT oligo Gal 02.gal

status: Public on Jan 27 2004

city: Newark

first: Xuelin

last: Cui

address: 185 S. Orange Ave.

department: Pharmacology and Physiology

institute: New Jersey Medical School-UMDNJ

description:
Rat 5K gene array

I. Array Design Description
In this study, a commercially available 5000 rat oligonucleotide array (CAG, ICPH, Newark, NJ) was employed. Please refer to the websites www.cag.icph.org and www.ngelab.org  about the detailed array design elements.

The following information was required by the  MGED:
1.	Array related information: array design name: Rat 5K Oligo Array (NGEL 2.01); platform type: spotted; surface and coating specification: flat, silicon coating; physical dimensions of array support: glass slide; number of features on the array: about 5000; availability: commercial arrays.
2.	a) For each reporter type: single stranded synthetic 60-70 base oligo-
nuceotides.
b) For each reporter: sequence, lengths, and element generation
protocol information: please require from manufacturer or refer to
its website.
3.	a) For each feature type: dimensions.
b) For each feature: refer to the manufacturer's website.
4.	For each composite sequence: refer to the manufacturer's website.
5.	Control elements on the array: position of the feature: refer to the manufacturer's website; control type: negative and positive; control qualifier: endogenous.

The Neuroscience Gene Expression Laboratory (NGEL) 2.01 Rat Oligo arrays were purchased from the Center for Applied Genomics (CAG), International Center for Public Health (ICPH), Newark, NJ. The arrays are mainly built from two groups of oligonucleotides: the complete Compugen C-GEN Rat library (4,854 oligos representing 4,803 independent genes and over 9,225 independent mRNAs) and a custom-designed set based on suggestions from our collaborators (approximately 120 oligos). The total gene number is about 5000, so it is also called 5 k rat oligo array. All oligos are 60-70 nt, and are 5' amine linked to aldehyde modified slides.  The array also contains a number of custom-designed controls, including random sequence negative probe, random sequence matching a Cy3-labeled complement positive control, common rat pathogen sequences, green fluorescent protein gene probe and a scale of 8:1 to 1:8 molar ratios of Genisphere capture sequences.

This array contains the Compugen C-GEN Rat library, as well as over 100 custom-synthesized rat probes.

first: Xue-Lin

first: Patricia

last: Soteropoulos

last: Tolias

first: Ronaldo

last: Ferraris


title: Atlas Glass Human 3.8 II Microarray (Cat. #7910-1)

status: Public on Oct 01 2002

city: Palo Alto

last: BD Biosciences Clontech

state: CA

address: 1020 East Meadow Circle

country: USA

institute: BD Biosciences Clontech

organism: Homo sapiens

technology: spotted oligonucleotide

description: Glass microarrays made with long (~80 bp) experimentally-tested oligonucleotides.

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: Atlas Glass Human 3.8 I Microarray (Cat. #7903-1 & 7904-1)


title: Abeta-activated Microglia Part 1

status: Public on Oct 29 2003

city: South San Francisco

first: Scott

middle: Curtis

last: Lohr

address: 290 Utah Ave.

department: Bioinformatics

institute: AGY Therapeutics Inc.

technology: spotted DNA/cDNA

description:
RNA Preparation
Total RNA from abeta stimulated cells was isolated using Tri Star reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, CA).  The resulting RNA was treated with RNAse free DNAse (Ambion, Austin, Texas) for 40 minutes at 37.C.  Isolation of mRNA was carried out using Oligotex (Qiagen, Chatsworth, CA).
Library Generation
To construct the subtractive and normalized cDNA libraries, reverse transcription and second strand synthesis were performed using the Superscript II reverse transcription kit (Invitrogen, Carlsbad, CA) with an anchored Oligo dT (30) primer. Subtractive and normalized cDNA libraries were generated using suppression PCR.
Array Creation
Subtracted and normalized cDNA libraries were cloned into the pCR2.1 vector (Invitrogen, Carlsbad, CA), and plated. Single colonies were picked into 384 well plates using an automated colony picker (Q-Pix, Genetix, Cambridge, UK) to grow overnight and subsequently serve as templates for PCR. PCR products were spotted on Nylon membranes using a 384 pin head arrayer (Q-bot, Genetix, Cambridge, UK). The spotted PCR product on all filters were cross-linked to the membrane by UV light. Filters were neutralized and denatured using standard protocols.
Library Description
SL00097:3h abeta stimulated
SL00098:6h abeta stimulated
SL00099:12h abeta stimulated
Related Platforms
GPL562

distribution: non-commercial

first: L

last: Gan

first: S

last: Ye

first: A

last: Chu

first: K

last: Anton

last: Yi

first: V

last: Vincent

first: D

last: von Schack

last: Chin

first: J

last: Murray

last: Patthy

first: M

last: Gonzalez-Zulueta

last: Nikolich

first: R

last: Urfer


title: BLI_array_NIAS

status: Public on Oct 20 2003

city: Tsukuba City, Ibaraki

first: Chandana

last: Herath

address: Ikenodai 2

department: Development Biology

country: Japan

organism: Bos taurus

description:
BLI_array_NIAS platform of a spotted cDNA microarray has been established using a bovine liver cDNA library. The array has been fabricated collaboratively by Laboratory of Reproductive Biology and Technology at National Institute of Agrobiological Sciences, Tsukuba Science City, Japan and Department of Paediatric Pharmacology at National Institute of Child Health and Development, Tokyo, Japan.
Keywords = bovine liver, cDNA array, gene expression

middle: B

first: Satoshi

last: Shiojima

first: Hiroko

last: Ishiwata

first: Susumu

last: Katsuma

first: Tadashi

last: Kadowaki

first: Koichi

last: Ushizawa

first: Kei

last: Imai

first: Toru

last: Takahashi

first: Akira

last: Hirasawa

first: Gozoh

last: Tsujimoto

first: Kazuyoshi

last: Hashizume


title: Atlas Glass Human 1.0 Array (Cat. #7900-1)

last: BD Biosciences Clontech


title: ACF_SGF_CEA

status: Public on Mar 11 2003

city: Evry

first: Jerome

last: Lamartine

address: 2 rue Gaston Cremieux

department: Departement de Radiobiologie et Radiopathologie

country: France

institute: CEA

description:
A collection of 5760 full length cDNA clones from the human infant brain 1NIB library kindly gifted by Genethon as bacterial colonies in 96-well microtitre plates. These clones were characterized by 5' and 3' sequencing. Plasmids containing clones were grown in Escherichia coli by standard microbiological methods. Each insert was PCR amplified (30 cycles) by sampling 1 µl of cell culture with vector primers. To obtain a sufficient amount of probes, a second run of PCR, consisting of 20 cycles, was performed using the same set of primers. PCR products ranged from 600 to 4000 bp in length.
The PCR products were prepared in 96-well plates, purified by ethanol precipitation, washed in 70% ethanol, dried, dissolved in TE/DMSO (50/50) and stored at -80°C. PCR products were arrayed on amino-silane coated glass slide (Corning CMT-GAPS II) using a MicroGrid-II Micro-arrayer (BioRobotics, Cambridge, UK).
Keywords = cDNA array, PCR products

first: Pascal

last: Soularue

first: Amandine

last: Pitaval

first: Cyril

last: Petat

first: Olivier

last: Alibert

first: Sophie

last: Lemoine

first: Xavier

last: Gidrol


title: Ab Microarray 380 (Cat. #K1847-1)

technology: antibody

description: The BD Clontech Ab Microarray 380 is composed of 378 of distinct, well-characterized monoclonal antibodies covelently immobilized on a glass slide. The antibodies were selected for their specificities and their high binding affinities, and detect a wide variety of intracellular proteins, both cytosolic and membrane-bound, representing a broad range of functional classes.


title: Atlas Plastic Rat 4K Microarray (Cat. #7909-1)

organism: Rattus norvegicus

description: Plastic microarrays made with long (~80 bp) experimentally-tested oligonucleotides.


title: Atlas Plastic Mouse 5K Microarray (Cat. #7906-1)

organism: Mus musculus


title: Atlas Mouse cDNA Expression Array (Cat. #7741-1)

description: Nylon, broad-coverage murine cDNA array.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Plastic Human 8K Microarray (Cat. #7905-1)

description: Plastic microarrays made with long (~80 bp) experimentally-tested oligonucleotides.  Contains sequences from more than 8300 named genes.


title: Atlas Mouse Toxicology 1.2 Array (Cat. #7861-1)

description: Nylon, murine cDNA array designed to study toxicology.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Mouse Cancer 1.2 Array (Cat. #7858-1)

description: Nylon, murine cDNA array designed to study cancer.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Toxicology 1.2 Array (Cat. #7859-1)

description: Nylon, human cDNA array designed to study toxicology.  The genes were assembled in collaboration with the Environmental Protection Agency (EPA).  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Oncogene and Tumor Suppressor Array (Cat. #7745-1)

description: Nylon, human cDNA array designed to study oncogenes and tumor suppressors.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Mouse Stress Array (Cat. #7749-1)

description: Nylon, murine cDNA array designed to study stress.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Neurobiology Array (Cat. #7736-1)

description: Nylon, human cDNA array designed to study neurobiology.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Cell Interaction Array (Cat. #7746-1)

description: Nylon, human cDNA array designed to study cell interactions.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Cancer cDNA Expression Array (Cat. #7742-1)

description: Nylon, human cDNA array designed to study cancer.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human Cell Cycle Array (Cat. #7748-1)

description: Nylon, human cDNA array designed to study cell cycle.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Human 1.2 Array III (Cat. #7855-1)

description: !Platform_description = Nylon, broad-coverage human cDNA array.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.


title: Atlas Glass Mouse 3.8 I Microarray (Cat. #7907-1)

description: Glass microarrays made with long (~80 bp) experimentally-tested oligonucleotides.


title: Atlas Glass Rat 1.0 Array (Cat. #7902-1)


title: Atlas Human Apoptosis Array (Cat. #7743-1)

description: Nylon, human cDNA array designed to study apoptosis.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.