Project description:This study intends to explore the clinicopathological characteristics and survival prognosis of locally recurrent colorectal cancer patients with different treatment modes by retrospectively analyzing the medical records of locally recurrent colorectal cancer patients who received hospitalization in our center. Transcriptome sequencing and public databases were used to screen for molecular markers related to locally recurrent colorectal cancer and to explore molecular markers’ regulatory role in the progression of locally recurrent colorectal cancer.
Project description:. Here we provide a deeper insight into Xenopsylla cheopis salivary glands contents pairing transcriptome and proteomic approaches. Sequencing of 99 pairs of salivary glands from adult females X. cheopis yielded a total of 7,432 coding sequences functionally classified into 25 classes, in which the secreted class was found to be the most abundant one. The translated transcripts also served as a reference database for the proteomic study, which identified peptides from 610 different proteins.
Project description:Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the proteome-scale. However, most proteomic studies remain limited to the analysis of canonical reference proteomes. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2.
Project description:Validation of Lactobacillus plantarum WCFS1 transcriptome profile using RNA sequencing (direct cDNA sequencing and 3'-UTR sequencing) in comparison with DNA microarray as a reference platform.
Project description:Proteomics data from a combind transcriptome/proteome study of three sexually deceptive orchids of the genus Ophrys. Data are from labella of mature, unpollinated flowers of (1) Ophrys exaltata subsp. archipelagi, (2) O. sphegodes, and (3) O. garganica. Proteomics data were searched against SwissProt and TAIR databases and further against organism-specific databases obtained from transcriptome sequencing (454, Sanger ESTs and Solexa data). Thirteen trypsinised gel slices per sample were subjected to electrospray ionisation-based LC-MS/MS analysis with a 2D linear ion trap Finnigan LTQ (Thermo Electron Corporation) equipped with an Ultimate Nano HPLC System (Dionex Corporation). Mass spectra were searched against SwissProt and Arabidopsis TAIR9 protein databases to identify peptides. Additionally, spectra were searched against protein databases created from the Ophrys reference transcriptome obtained in this study. Stringent criteria were used for the assignment of spectra to peptides (95% peptide identification probability) in Scaffold 3.3 (Proteome Software Inc., USA). In order to maximise the utility of proteomics data for uncovering proteins predicted by the orchid transcriptome, a minimum of one unique peptide was used for protein identification, while using two different stringency levels for the probabilistic assignment of peptides to proteins (99% for highest quality, HQ; 90% to maximise protein discovery, PD, in the absence of a fully sequenced genome). Concerning the sequencing and transcriptomics results: Three normalised cDNA libraries were constructed from three different Ophrys species, O. exaltata, O. garganica, and O. sphegodes. These libraries were 454 pyrosequenced and all the high quality reads generated in this study are available in the Sequence Read Archive (SRA) of the National Centre for Biotechnology Information (NCBI) with the accession number SRA060767. Additional sequencing of O. sphegodes flower labella yielded 1.7 Mbp of Sanger (dbEST library LIBEST_028084; dbEST IDs 77978749-77979571; GenBank accessions JZ163765-JZ164587) and 2.5 Gbp of Illumina Solexa (SRA060767) data.
Project description:We developed a transcriptome resource for Douglas-fir covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. Extracted RNA was sequenced using large-scale sequencing and reads were assembled to generate a de novo reference transcriptome of 105,505 predicted high-confidence transcripts. Expression levels were estimated based on alignment of the original reads to the reference.
Project description:Intellectual disability is a common condition that carries lifelong severe medical and developmental consequences. The causes of intellectual disability (ID) remain unknown for the majority of patients due to the extensive clinical and genetic heterogeneity of this disorder. De novo mutations may play an important role in ID as most individuals with ID present as isolated cases without family history and/or clear syndromic indication. In addition, the involvement of such mutations have recently been demonstrated in a small number of individuals with ID. Here we evaluate the diagnostic potential and role of de novo mutations in a cohort of 100 patients with ID of unknown cause using family-based exome sequencing. Single end short-read (50 bp) SOLiD 4 sequencing data for 300 individuals, constituting 100 patient-parent trios. For more details please read; http://www.nejm.org/doi/full/10.1056/NEJMoa1206524. Dataset is created by RUNMC (Radboud University, Nijmegen Medical Center), partner of Geuvadis consortium (http://www.geuvadis.org).