Rat kangaroo (Ptk cells!) transcriptome PAPER:
Udy DB, Voorhies M, Chan PP, Lowe TM, Dumont S. Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PLoS One 10: e0134738 (2015). [PDF]
Abstract:
The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes—and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics.
Rat kangaroo transcriptOME ANALYTICS PLATFORM:
This browser displays different Trinity transcripts using a the UCSC Banana Slug Analytics Platform, where mRNA transcripts have been substituted for chromosomes. Trinity transcripts are assembled and numbered (but not annotated), and a BLAT search tool enables mapping of any input protein or nucleotide sequences to the rat kangaroo transcriptome. [Login & password info in Quick Start Guide below.]
Rat kangaroo TRANSCRIPTOME EXPLORER:
This browser contains transcript information including sequence and analysis (protein detail, BLASTP FPKM, etc.). A search tool allows the user to search for rat kangaroo transcripts by gene description, or transcript ID (from above browser). [Open access]
QUICK START GUIDE:
Updated in July 2020. Contact renaldo.sutanto@ucsf.edu or sophie.dumont@ucsf.edu with any questions.