GBC-Long-read-Transcriptome

A Novel ERBB2 Alternative Splicing Variant Induces Drug Resistance in Gallbladder Cancer Revealed by Long-read Transcriptome Sequencing

we employed the advanced long-read full-length transcriptome sequencing technology on GBC, normal tissues, and cell lines to establish a comprehensive transcriptomic atlas. One isoform with a novel exon was identified designated as ERRB2 i14e in multiple independent GBC datasets involving 179 GBC cases and the expression of ERRB2 i14e was associated with disease worse prognosis.

Pacbio CCS data prrocessing

Refer to the official website and follow the step-by-step process

isoseq3

https://isoseq.how/clustering/cli-workflow.html

Followed by Cupcake：

https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake:-supporting-scripts-for-Iso-Seq-after-clustering-step

Followed by SQANTI3：

https://github.com/ConesaLab/SQANTI3

For Interchromosomal fusion transcripts

We used FusionSeeker (v1.0.1) to identify interchromosomal fusion transcripts. Next, we selected the confident_genefusion_transcript_sequence.fa files and used BLAST to manually verify the correct fusion transcripts.