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Strain-specific cortex gene expression and isoform usage

Differential gene expression and transcript isoform analysis between C57BL/6J and DBA/2J mouse cortex tissue using Oxford Nanopore PCR-cDNA long-read sequencing. Three biological replicates per strain, with AMPure XP bead size selection at 1.5 kb cutoff.

Samples

69 samples

69 Sample Prep
  • C57_DBA_pool_run3 — Equimolar pooling of C57/DBA re-barcoded PCR-cDNA libraries (run 3)
  • DBA_rep3_bc15 — PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15)
  • DBA_rep2_bc14 — PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15)
  • DBA_rep1_bc13 — PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15)
  • C57_rep3_bc12 — PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15)
  • C57_rep2_bc11 — PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15)
  • …and 63 more
Assay Workflows
Completed
PacBio CCS (Subreads → HiFi)
Data Transformation: PacBio CCS (Subreads → HiFi) (Run #78) succeeded
IsoSeq Clustering (Refine + Cluster)
Data Transformation: IsoSeq Clustering (Refine + Cluster) (Run #83) succeeded
IsoSeq Annotation (Map + Collapse + SQANTI3)
Data Transformation: IsoSeq Annotation (Map + Collapse + SQANTI3) (Run #93) succeeded
Functional Annotation (TransDecoder + Pfam + SwissProt)
Data Transformation: Functional Annotation (TransDecoder + Pfam + SwissProt) (Run #103) succeeded
Completed
PacBio CCS (Subreads → HiFi)
Data Transformation: PacBio CCS (Subreads → HiFi) (Run #77) succeeded
IsoSeq Clustering (Refine + Cluster)
Data Transformation: IsoSeq Clustering (Refine + Cluster) (Run #82) succeeded
IsoSeq Annotation (Map + Collapse + SQANTI3)
Data Transformation: IsoSeq Annotation (Map + Collapse + SQANTI3) (Run #92) succeeded
Functional Annotation (TransDecoder + Pfam + SwissProt)
Data Transformation: Functional Annotation (TransDecoder + Pfam + SwissProt) (Run #102) succeeded
Completed
PacBio CCS (Subreads → HiFi)
Data Transformation: PacBio CCS (Subreads → HiFi) (Run #76) succeeded
IsoSeq Clustering (Refine + Cluster)
Data Transformation: IsoSeq Clustering (Refine + Cluster) (Run #81) succeeded
IsoSeq Annotation (Map + Collapse + SQANTI3)
Data Transformation: IsoSeq Annotation (Map + Collapse + SQANTI3) (Run #91) succeeded
Functional Annotation (TransDecoder + Pfam + SwissProt)
Data Transformation: Functional Annotation (TransDecoder + Pfam + SwissProt) (Run #101) succeeded
Completed
Completed
Completed
Mouse Long-Read RNA-Seq (ONT PCR-cDNA)
Data Transformation: Mouse Long-Read RNA-Seq (ONT PCR-cDNA) (Run #4) succeeded
Data Transformation: Mouse Long-Read RNA-Seq (ONT PCR-cDNA) (Run #6) succeeded
ONT Long-Read Transcriptomics (IsoQuant)
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #42) succeeded
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #43) succeeded
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #44) succeeded
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #45) succeeded
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #46) succeeded
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #47) succeeded
ONT Isoform Functional Annotation (superseded)
Data Transformation: ONT Isoform Functional Annotation (superseded) (Run #48) succeeded
Data Transformation: ONT Isoform Functional Annotation (superseded) (Run #49) succeeded
Data Transformation: ONT Isoform Functional Annotation (superseded) (Run #50) succeeded
Data Transformation: ONT Isoform Functional Annotation (superseded) (Run #51) succeeded
Data Transformation: ONT Isoform Functional Annotation (superseded) (Run #52) succeeded
ONT Long-Read Transcriptomics (IsoQuant)
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #41) failed
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #109) canceled
Functional Annotation (TransDecoder + Pfam + SwissProt)
Data Transformation: Functional Annotation (TransDecoder + Pfam + SwissProt) (Run #110) canceled
ONT Long-Read Transcriptomics (IsoQuant)
Data Transformation: ONT Long-Read Transcriptomics (IsoQuant) (Run #111) failed
Completed
Completed
Measurement 2
Sample Preparation 9
Other 1
Management 1
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