Project description:We consturcted a full-length transcript reference of CD4SP and CD8SP T cells using TGS (PacBio) data. We then used SGS (Illumina) CD4SP and CD8SP data to quantify isoform expressions and study alternative splicing patterns against the full-length transcript reference between CD4SP and CD8SP cells.
Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.
Project description:A novel alternative splicing isoform of LOXL2 △e13 was expressed ubiquitously in all cell lines and ESCC tissues. In contrast to the impaired deamination enzymatic activity compared with full length LOXL2, LOXL2 △e13 showed an enhanced ability to promote cell mobility and invasiveness in ESCC cells than full length LOXL2 through a different mechanism.
Project description:To analyse the regulation of transcripts in grain embryo and endosperm during development, we performed RNA-Seq for wheat from 14 and 25 day post anthesis (DPA). And long-read sequencing for mixed whole grains from 14 and 25 DPA was employed to obtain full-length transcripts. A series of differentially expressed genes and tissues-specific genes of embryo and endosperm were identified. Moreover, 4351, 4641, 4516 and 4453 genes with A, B and D homoeoloci were detected in the four tissues. These provide specific gene pools of embryo and endosperm and homoeolog expression bias model in a large scale, which provides new insights into the molecular physiology of wheat.
Project description:To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of lung adenocarcinoma cell lines using a long-read sequencer MinION. We constructed a comprehensive catalog of aberrant splicing isoforms and detected isoform-specific peptides using proteome analysis.
Project description:Single-cell isoform regulation is increasingly being studied. To get a full view of alternative isoform usage, from transcription start site and alternative splicing to transcription termination site, full-length sequences have to be studied. Here we use PacBio long read sequencing technology combined with unique molecular identities to get a full and accurate picture of alternative isoform usage of different stages in maturing oligodendrocyte single cells. We see that the majority of molecules in single-cells are separate isoforms, even after applying a conservative definition of what constitutes an isoform. Few isoforms are common between cells of the same cell-type but the common isoforms are higher expressed. We also see that exon junctions in coding regions are better regulated than exon junctions in non-coding regions and that genes often express more than one coding isoform.