Similar Datasets
Project description:Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.
2023-07-20 | GSE211836 | GEO
Project description:Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.
2023-05-04 | GSE179744 | GEO
Project description:Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.
2023-09-07 | PXD029392 | Pride
Project description:Sjögren's Syndrome (SS) is an autoimmune exocrinopathy characterized by the progressive damage of salivary and lacrimal glands associated with lymphocytic infiltration. It can be defined as primary SS (pSS) or associated/secondary SS (sSS) if combined with another systemic autoimmune disease. Identifying new non-invasive biomarkers for SS diagnosis remains a challenge, and alterations in saliva composition reported in patients turn this fluid into a source of potential biomarkers. To examine the overall panorama of proteins in saliva, samples of control, pSS, and sSS individuals were analyzed by gel-free LC-MS/MS.
2021-06-09 | PXD025434 | Pride
Project description:Sjögren's Syndrome (SS) is an autoimmune exocrinopathy characterized by the progressive damage of salivary and lacrimal glands associated with lymphocytic infiltration. It can be defined as primary SS (pSS) or associated/secondary SS (sSS) if combined with another systemic autoimmune disease. Identifying new non-invasive biomarkers for SS diagnosis remains a challenge, and alterations in saliva composition reported in patients turn this fluid into a source of potential biomarkers. To examine the overall panorama of proteins in saliva, samples of control, pSS, and sSS individuals were analyzed by gel-based LC-MS/MS.
2021-06-09 | PXD025463 | Pride
Project description:Interventions: Patients in the treatment group were treated by moxibustion therapy once every other day, 3 times a week for 6 weeks in total. Moxa rolls provided by Nanyang Chinese Medicine Airong Co. LTD (Henan, China) were used in the trial. Points of Shenque (CV 8), Tianshu (ST25), and Zusanli (ST36) were selected for moxibustion in the supine position.;Experimental Other;moxibustion therapy
Primary outcome(s): IBS-SSS from week 0 to week 6 6 weeks changes in total IBS-SSS from week 0 to week 6
| 27658 | ecrin-mdr-crc
Project description:This study aimed to analyze the mutated genes of primary and recurrent SSs (PRSSs), to discover whether these sarcomas exhibit some potential mutated genes between primary and recurrent cases Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples.
2021-06-25 | GSE178828 | GEO
Project description:Here we introduce STORM-seq, a standardized and generally available approach to profiling total RNA in single cells by miniaturization of the Takara SMART-seq Stranded (SSS) kit. The use of nanoliter-scale reaction volumes allows STORM-seq to efficiently scale to hundreds of high-complexity single cell libraries per run, from dissociated tissues and non-adherent cells, with greater than 99% per cell/library success. The use of ribosomal RNA depletion and random hexamer priming, rather than oligo-dT (poly-A) selection, allows comprehensive, whole-transcriptome analysis in each individual cell. STORM-seq recovers both coding and non-coding transcripts at an equal or greater rate to full volume reactions. Applying the method to cultured K562 cells and primary human fallopian tube epithelial (FTE) cells results in equivalent or better gene detection than manual preparation. Across all transcript biotypes, additional mRNA and lncRNA transcripts are detected beyond SSS or SMART-seq2. STORM-seq libraries from primary human FTE reveal intermediate cell types not observed by other technologies, with clear transitional significance visible upon data integration. STORM-seq provides a scalable, efficient protocol to recover deep whole transcriptomes from individual cells while minimizing costs.
2022-08-05 | GSE181544 | GEO