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View additional product information for Clariom™ D Assay, rat - FAQs (902633, 902634)
10 product FAQs found
Tough-Spots® labels are small adhesive stickers used to temporarily seal the backs of cartridge arrays during the overnight hybridization step. They are required to prevent loss of volume due to evaporation through the septa. We recommend using Tough-Spots® labels on Rolls from USA Scientific (Item No. 9185-0000)
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Proper hybridization volume is critical to obtaining an even signal across a given array. Too little volume can lead to black circles in the middle of the array. Too much volume can leak out of the back of the array. The correct hybridization volume leaves enough room for a small air bubble to circulate around the array surface during the overnight hybridization. Here are the recommended hybridization and fill volumes based on the array format:
Array Format; Hybridization Volume; Fill Volume
- 49 Format (Standard); 200 µL; 250 µL
- 64 Format; 200 µL; 250 µL
- 100 Format (Midi); 130 µL; 160 µL
- 169 Format (Mini); 80 µL; 100 µL
- 400 Format (Micro); 80 µL; 100µL
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Clariom D arrays have probes that cover all known regions of transcription including probes in overlapping regions from both strands. To obtain strand-specific information from the Clariom D arrays, the WT Pico and WT Plus reagents (which are strand-specific) must be used. This is important because without strand-specific reagent, it would not be possible to decipher the source strand of DNA, which makes it challenging to untangle true gene- and exon- level expression and alternative splicing events.
Strand-specificity is significantly less important for customers interested in gene-level only information (i.e., those using Clariom S) as compared to customers who want to understand the complexities of the whole transcriptome including identifying antisense transcripts and ncRNA (i.e., those using Clariom D). While strand-specificity is less important for gene-level expression only, probes within regions of overlapping transcription from both strands are avoided in the Clariom S array design (unlike Clariom D). This is important because if Clariom S did not preserve strand-specificity, there could be an overestimation of gene-level expression causing false positive or negative results. With Clariom S having a "stranded" design, it does not necessarily need a strand-specific reagent kit.
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Analysis library files and annotation files can be downloaded from within the TAC Software. Please refer to the respective user manuals for detailed instructions.
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Probe cell intensity data (CEL) from human, mouse, or rat transcriptome assays are analyzed in Transcriptome Analysis Console(TAC) Software. The application uses a version of RMA analysis to create CHP files. Transcriptome Analysis Console Software can be downloaded at no charge from the website. Further statistical analysis may be performed in Affymetrix' Transcriptome Analysis Console (TAC) Software to obtain a list of differentially expressed genes and alternative splicing events. TAC Software also provides the visualization of genes, exons, junctions, transcript isoforms, pathways, and mRNA-miRNA regulatory networks.
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To install library files for the human, mouse, or rat transcriptome arrays for AGCC, simply run the executable library file installer.
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Human, mouse, or rat transcriptome arrays are 49-format.
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FS450_0001 should be used when processing human, mouse, or rat transcriptome assays. Up-to-date fluidics scripts can be obtained from the website.
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Human, mouse, or rat transcriptome assays utilize an updated installer package that is not compatible with GCOS. Human, mouse, or rat transcriptome assays require AGCC for fluidics and scanning. The Expression Console Software is required to perform QC analysis of the human, mouse, or rat transcriptome array data. Expression Console Software can be downloaded at no charge from the website.
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Affymetrix human, mouse, and rat transcriptome assays are available in three formats based on sample type and amount of input RNA:
Human, mouse, and rat transcriptome Pico assays compatible with 100-2,000 pg of RNA isolated from fresh, frozen, blood, or FFPE samples
Human, mouse, and rat transcriptome FFPE assays compatible with 20-200 ng of RNA isolated from FFPE samples
Human, mouse, and rat transcriptome assays compatible with 50-500 ng of RNA isolated from fresh, frozen, or blood samples
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