| Type: | in situ hybridisation probe |
| Identifier: | MGI:3696422 |
| Entity Detected: | Usp42, ubiquitin specific peptidase 42 ( MGI:1924050) |
| Notes: | The Usp42 probe used in this study by Kim et al., 2007 [PMID:16904385] is described as follows: "For Northern blot analysis, the immobilized nucleic acids were hybridized with a radiolabeled DNA probe corresponding to 720 bp of the Usp42 clone. The probe was prepared using two primers designed as following: Usp42/F (5'-TTGTATGCTGTGCTGGTG-3') or Usp42/R (5'-GCCTTGCCGTTCACCATG-3'). For in situ hybridization, riboprobes were synthesized from linearized plasmids containing the nucleotides from 1063 to 1782 bp of Usp42 cDNA using digoxygenin-labeled UTP (Roche) and in vitro transcription kits (Promega). To generate an antisense probe, Usp42 was linearized using SalI and transcribed using SP6 RNA polymerase."
Editors note: Elsewhere in the manuscript, the authors describe their strategy for cloning the Usp42 cDNA, which used primers designed to isolate the 'full length' of Usp42 from the start codon to stop codon, therefore the nucleotide numbering the authors use in describing the in situ hybridisation probe start and end positions, relate to the ORF alone. The two primers Usp42/F and Usp42/R listed above amplify this same region, which within the Usp42 mRNA RefSeq NM_029749.2, corresponds to nt1190-1899. SalI cuts within this region at nt 1849 (relative to NM_029749.2), which suggests the antisense probe would be 50nt in length. Ambiguous information.
NB. The authors also state that sense probe was generated by linearisation of the Usp42 cDNA with EcoRV, which cuts NM_029749.2 at nt1309, indicating that this probe would be 119nt in length and non-overlapping with the antisense probe. |
| Chemistry: | RNA |
| Strand: | antisense |
| Label: | digoxigenin |
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