Methodology

Microarrays

The following listings provide links and information regarding NIEHS Microarray Group protocols, equipment, software, and arrays.

Protocols

RNA

• RNA Preparation
  • RNA Preparation from Cultured Cells (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna_cul_cell.pdf)   (46KB)
  • RNA Preparartion from Animal Tissues (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna_animal.pdf)   (23KB)
  • Specialized RNA Preparation Protocols
    • From Blood
      • Human (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/paxgene_human_blood.pdf)   (85KB)
      • Rat (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/paxgene_ratblood.pdf)   (83KB)
    • From Skin (Mouse) (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna_mouse_skin.pdf)   (26KB)
    • From Heart (rodent) (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna_rodent_heart.pdf)   (44KB)
  • RNA Preparation from LCM and Small Amounts of Tissue (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna-lcm-arcturus.pdf)   (29KB)
• Tissue Collection (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rna_tissue_collection_protocol.pdf)   (77KB)
• Tissue Pulverization (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/pulveriz-proto.pdf)   (60KB)
• Post-BioAnalyzer RNA Clean-up (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/PostBioAnalyzerRNAcleanup.pdf)   (60KB")
• Post-BioAnalyzer DNase Treatment and Cleanup of RNA (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/PostBioAnalyzerDNaseTxRNA.pdf)   (64KB")

Labeling and Hybridization

• Agilent Reverse Transcription Labeling and Probe Hybridization Protocol (Direct or Low Input Amplification)(http://www.chem.agilent.com/scripts/generic.asp?lpage=14919&indcol=Y&prodcol=Y)
• Affymetrix Genechip® Expression Analysis Technical Manual for One-Cycle and Two-Cycle Target Labeling Assays (Free registration required)(http://www.affymetrix.com/support/technical/manual/expression_manual.affx)
• Reverse Transcription Labeling and Probe Hybridization Protocol (Cy-dUTP) (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/rtlabel.pdf)   (94KB)
• Reverse Transcription Labeling and Probe Hybridization Protocol (Cy-dCTP) (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/cy-dctp.pdf)   (70KB)

Scanning & Image Analysis

• Scanning Using the Agilent Scanner(http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=33696)
• Scanning Using the Affymetrix Scanner (http://www.affymetrix.com/support/downloads/quick_reference_cards/gcs3000_qrc.pdf)  

Printing

• Processing of Slides Prior to Printing (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/ppl.pdf)   (60KB)
• Processing of Slides Post-Printing (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/slides_postprocess.pdf)   (79KB)
• QA/QC of Prints (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/qc_printing.pdf)   (82KB)
• POPO3 DNA Staining for Microarray Slides (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/popo_stain.pdf)   (65KB)

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Equipment

• Agilent Bioanalyzer
• Robbins Scientific Tango Liquid Handling System
• Beecher Instruments Microarray Printer
• Agilent Scanners
• NanoDrop
• Affymetrix GeneChip® Instrument
• MAUI Hybridization Station
• Applied Biosystems 7500 Real Time PCR System

Software

• GeneSpring
• Rosetta Resolver
• Ingenuity Pathways Analysis
• Partek
• CGH Analytics
• CHip Analytics
• Feature Extraction
• Genepix

Arrays

• Gene Expression
  • Agilent(http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494)
  • Affymetrix(http://www.affymetrix.com/products/arrays/index.affx)
  • Illumina
• ChIP-on-Chip
  • Agilent(http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494)
• Exon
  • Affymetrix(http://www.affymetrix.com/products/arrays/index.affx)
• aCGH
  • Agilent(http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494)
• miRNA
  • In-house arrays using Ambion’s mirVana miRNA probe set(http://www.ambion.com/catalog/ProdGrps.html?fkApp=29&fkSubApp=176)
• Mapping
  • Affymetrix(http://www.affymetrix.com/products/arrays/index.affx)

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