PMC:7572125 / 13796-15745
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7572125","sourcedb":"PMC","sourceid":"7572125","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7572125","text":"To test if sequestration of the putative PTEN ceRNAs impacted PTEN expression, we ectopically overexpressed the 3’UTR of the same putative PTEN ceRNAs as the original study in DU145 cells along with the Luc-PTEN-3’UTR plasmid. This is similar to what was reported in Figure 3D of Tay et al., 2011 and described in Protocol 2 in the Registered Report (Phelps et al., 2016). We used the same plasmids as the original study, which cloned the 3’UTRs of VAPA and CNOT6L as two separate fragments due to their large size with the fragments subdivided based on location of predicted MREs (Tay et al., 2011). We found that compared to cells transfected with empty vector control, cells transfected with 3’UTR of the putative PTEN ceRNA plasmids or the 3’UTR of PTEN had decreased luciferase activity (Figure 2, Figure 2—figure supplement 1). The planned comparisons were statistically significant for SERINC1 3’UTR, VAPA 3’UTR2, CNOT6L 3’UTR1, CNOT6L 3’UTR2, and PTEN 3’UTR1, but not for VAPA 3’UTR1 (see Figure 2 legend). The original study reported statistically significant increased luciferase activity with SERINC1 3’UTR (average RLU = 128%), VAPA 3’UTR1 (average RLU = 141%), VAPA 3’UTR2 (average RLU = 150%), CNOT6L 3’UTR1 (average RLU = 143%), CNOT6L 3’UTR2 (average RLU = 146%), or PTEN 3’UTR (average RLU = 153%) compared to empty vector control (average RLU = 100%) (Tay et al., 2011). The range of luciferase values reported in the original study had RSDs (control = 9%; SERINC1 3’UTR = 9%; VAPA 3’UTR1 = 13%; VAPA 3’UTR2 = 6%; CNOT6L 3’UTR1 = 7%; CNOT6L 3’UTR2 = 7%; PTEN 3’UTR = 1%) that were smaller than the RSDs observed in this replication attempt (control = 17%; SERINC1 3’UTR = 12%; VAPA 3’UTR1 = 12%; VAPA 3’UTR2 = 15%; CNOT6L 3’UTR1 = 15%; CNOT6L 3’UTR2 = 14%; PTEN 3’UTR = 10%). To summarize, we found results that were statistically significant (with the exception of VAPA 3’UTR1) and in the opposite direction as the original study.","tracks":[{"project":"2_test","denotations":[{"id":"33073769-22000013-27525619","span":{"begin":292,"end":296},"obj":"22000013"},{"id":"33073769-26943900-27525620","span":{"begin":366,"end":370},"obj":"26943900"},{"id":"33073769-22000013-27525621","span":{"begin":594,"end":598},"obj":"22000013"},{"id":"33073769-22000013-27525622","span":{"begin":1382,"end":1386},"obj":"22000013"}],"attributes":[{"subj":"33073769-22000013-27525619","pred":"source","obj":"2_test"},{"subj":"33073769-26943900-27525620","pred":"source","obj":"2_test"},{"subj":"33073769-22000013-27525621","pred":"source","obj":"2_test"},{"subj":"33073769-22000013-27525622","pred":"source","obj":"2_test"}]},{"project":"MyTest","denotations":[{"id":"33073769-22000013-27525619","span":{"begin":292,"end":297},"obj":"22000013"},{"id":"33073769-26943900-27525620","span":{"begin":366,"end":370},"obj":"26943900"},{"id":"33073769-22000013-27525621","span":{"begin":594,"end":598},"obj":"22000013"},{"id":"33073769-22000013-27525622","span":{"begin":1382,"end":1386},"obj":"22000013"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"33073769-22000013-27525619","pred":"source","obj":"MyTest"},{"subj":"33073769-26943900-27525620","pred":"source","obj":"MyTest"},{"subj":"33073769-22000013-27525621","pred":"source","obj":"MyTest"},{"subj":"33073769-22000013-27525622","pred":"source","obj":"MyTest"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#b493ec","default":true},{"id":"MyTest","color":"#93ec9a"}]}]}}