Long-read and short-read isoform sequencing in breast cancer

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006596	The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.	NextSeq 500	25
EGAD00001006597	The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.	PacBio RS II Sequel	26
EGAD00001009514	These are the raw subreads bam files for the pacbio IsoSeq data	NextSeq 500 PacBio RS II Sequel	30

Publications	Citations
A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer. Veiga DFT, Nesta A, Zhao Y, Deslattes Mays A, Huynh R, Rossi R, Wu TC, Palucka K, Anczukow O, Beck CR, Banchereau J. Sci Adv 8: 2022 eabg6711	60
A widespread length-dependent splicing dysregulation in cancer. Zhang S, Mao M, Lv Y, Yang Y, He W, Song Y, Wang Y, Yang Y, Al Abo M, Freedman JA, Patierno SR, Wang Y, Wang Z. Sci Adv 8: 2022 eabn9232	17
FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues. Shi Q, Li X, Liu Y, Chen Z, He X, He X. Nucleic Acids Res 52: 2024 D124-D133	12
Alternative splicing of transposable elements in human breast cancer. Nesta A, Veiga DFT, Banchereau J, Anczukow O, Beck CR. Mob DNA 16: 2025 6	1
Alternative splicing generates HER2 isoform diversity underlying antibody-drug conjugate resistance in breast cancer. Guardia GDA, Dos Anjos CH, Rangel-Pozzo A, Dos Santos FF, Birbrair A, Asprino PF, Camargo AA, Galante PAF. Genome Res 35: 2025 1942-1958	3