Protocol detail

Xenopus Inner Ear Transcriptome Analysis

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Xenopus inner ear RNA was profiled using the Affymetrix GeneChip^®Xenopus laevis Genome 2.0 Array (Affymetrix) comprising more than 32,400 probe sets (Xl-PSIDs), representing over 29,900 X. laevis transcripts. Labeled antisense single-stranded cDNA was prepared from each RNA replicate using the Ovation^™ RNA Amplification System V2 in conjunction with the FL-Ovation^™ cDNA Biotin Module V2 (both from NuGEN), hybridized overnight and scanned using a GeneChip Scanner 3000 7G (Affymetrix). RNA and microarrays were processed at the MIT BioMicro Center.

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Virk S.M., Trujillo-Provencio C, & Serrano E.E. (2024). Transcriptomic Analysis Identifies Candidate Genes for Differential Expression during Xenopus laevis Inner Ear Development. bioRxiv.

Publication Preprint 2024

GeneChip®Xenopus laevis Genome 2.0 Array Ovation™ RNA Amplification System V2 FL-Ovation™ cDNA Biotin Module V2 GeneChip Scanner 3000 7G

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Variable analysis

independent variables

Xenopus inner ear RNA profiling

dependent variables

Xenopus laevis transcripts as measured by Affymetrix GeneChip Xenopus laevis Genome 2.0 Array

control variables

Labeled antisense single-stranded cDNA prepared from each RNA replicate using the Ovation™ RNA Amplification System V2 and FL-Ovation™ cDNA Biotin Module V2
Hybridization and scanning of microarrays using Affymetrix GeneChip Scanner 3000 7G

controls

No positive or negative controls were explicitly mentioned.

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