Project description:Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.
Project description:Primary hypothesis: Side-to-end anastomosis is non-inferior to colon J pouch for reconstruction after low anterior resection for rectal cancer in fecal incontinence (Wexner score).
Research questions: Are there differences between side-to-end anastomosis and colon J pouch in
* bowel function (fecal incontinence, frequency of bowel movements, rectal urgency, incomplete evacuation)
* quality of life
* sexual function
* urinary function
* postoperative complications
* operation time/ institutional costs
Project description:This study aims to investigate the efficacy of Guided Written Disclosure Protocol (GWDP) in promoting post-traumatic growth through a process of meaning reconstruction in cancer patients at the end of chemotherapy. Also, the intervention (GWDP) intends to reduce distress symptoms (i.e. intrusive thoughts, avoidance, depression and anxiety).
Project description:Rare cell populations—often comprising less than 0.01% of all cells—play crucial roles in development, aging, and disease, yet standard single-cell sequencing methods typically miss them. To address this gap, here we developed EnrichSci, a microfluidic‑free, combinatorial indexing platform that integrates Hybridization Chain Reaction-RNA FISH with the high‑throughput EasySci pipeline for targeted cell enrichment and scalable single‑cell RNA sequencing. EnrichSci uses FACS to selectively enrich nuclei labeled by custom transcript modules and delivers full gene body coverage at under $0.001 per cell and tens of millions of cells per run. We applied EnrichSci to map the full oligodendrocyte lineage, uncovering age-related loss of precursor states and expansion of reactive mature subpopulations (C4b⁺ Serpina3n⁺). Through gene- and exon- level differential analyses, we revealed subtype-specific molecular changes in aging. In summary, by coupling transcript-guided enrichment with ultra scalable single-cell sequencing platform, EnrichSci offers a versatile approach for decoding the dynamic regulatory landscapes in rare cell types across diverse tissues and conditions.
Project description:The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. Gene ontology was performed on differentially expressed transcripts based on time-from-injury (acute, <3 months; intermediate, 3-12 months; chronic, >12 months). A subset of transcripts was validated via microfluidic digital polymerase-chain-reaction. Expression of periostin, a highly differentially expressed transcript, was tested by immunohistochemistry. Numerous transcripts covering important functional classifications were differentially expressed by time-from-injury. In acute tears, processes representing angiogenesis were repressed while those representing stem-cell differentiation were elevated. In intermediate tears, processes representing stem-cell proliferation concomitant with cellular component organization/cellular localization were elevated. In chronic tears, processes denoting myosin filament organization were elevated while those representing cellular component organization/cell localization and extracellular matrix organization were repressed. Expression levels of periostin were down-regulated in chronic tears compared to acute (42-fold) and intermediate (29-fold) tears. Immunohistochemistry confirmed a decline in periostin expression in tissues from chronic tears. These findings suggest an initial attempt of the injured ACL to repair, which declines with time-from-injury. These findings have implications for efforts to repair the ACL and may be relevant for reconstruction of the ACL. The functional role of periostin in ACL injuries, and the potential implication for surgical treatment, warrants further investigation. Total RNA obtained frominjured anterior cruciate ligament (ACL) tissues from pateints undergoing ACL surgery.
Project description:The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. Gene ontology was performed on differentially expressed transcripts based on time-from-injury (acute, <3 months; intermediate, 3-12 months; chronic, >12 months). A subset of transcripts was validated via microfluidic digital polymerase-chain-reaction. Expression of periostin, a highly differentially expressed transcript, was tested by immunohistochemistry. Numerous transcripts covering important functional classifications were differentially expressed by time-from-injury. In acute tears, processes representing angiogenesis were repressed while those representing stem-cell differentiation were elevated. In intermediate tears, processes representing stem-cell proliferation concomitant with cellular component organization/cellular localization were elevated. In chronic tears, processes denoting myosin filament organization were elevated while those representing cellular component organization/cell localization and extracellular matrix organization were repressed. Expression levels of periostin were down-regulated in chronic tears compared to acute (42-fold) and intermediate (29-fold) tears. Immunohistochemistry confirmed a decline in periostin expression in tissues from chronic tears. These findings suggest an initial attempt of the injured ACL to repair, which declines with time-from-injury. These findings have implications for efforts to repair the ACL and may be relevant for reconstruction of the ACL. The functional role of periostin in ACL injuries, and the potential implication for surgical treatment, warrants further investigation.
Project description:Protein band obtained from the Panax notoginseng leaves homogenate following an activity-guided protein-purification procedure, that showed regioselective ginsenoside hydrolysis activity was digested with trypsin and analyzed by Nano LC-LTQ Orbitrap MS to construct a peptide library of accessible amino acid sequences. Subsequent mutual sequence alignment analysis between the peptide and transcript libraries identified three candidate genes.