SpliMLib
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33942 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3474167.fastq.gz | Fastqsanger.gz |
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Project description:We describe a new generalizable library generation chemistry with increased efficiency that is amendable to tagmentation-based split-pool barcoding strategies, such as single-cell combinatorial indexing (sci). Symmetrical strand sci (‘s3’) uses a novel uracil-based adapter switching approach that provides an improved rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-ATAC) to profile human cortical and mouse whole brain tissues, with mouse datasets demonstrating a 6-to-13-fold improvement in usable reads obtained per cell when compared to other available methods performed on the same sample type. We also demonstrate the generalizability of s3 by applying it to single-cell whole genome sequencing (s3-WGS), and whole genome plus chromatin conformation (s3-GCC), for structural variant calling in a patient-derived cancer cell line model. Using the high-coverage profiles produced by the s3 technologies we characterized preserved clonal structure and identified a putative subclone-specific translocation.
2021-05-28 | GSE174226 | GEO
Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.
2017-01-31 | E-MTAB-5167 | biostudies-arrayexpress
Project description:Here, we report a CRISPR/Cas12k-transposon-assisted genome engineering (CTAGE) method that allows for high-throughput site-specific mutagenesis in microbial genomes. Exploiting the powerful CTAGE technique, we construct a site-specific transposon mutant library focusing on all the possible transcription factors (TFs) in Pseudomonas aeruginosa, enabling comprehensive identification of essential genes and new factors for antibiotic resistance.
2021-08-10 | GSE164797 | GEO
Project description:Purpose: The goal of this study is to determine whether hepatic deletion of Wtapaffects chromatin accessibility. Methods: Each liver sample was pooled from three Wtap-HKO and Wtapflox/flox mice, respectively. Three independent biological replicates of each group were used for ATAC-seq. Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol. Results: The hepatic chromatin accessibility in Wtapflox/flox and Wtap-HKO mice were characterized.
2022-06-02 | GSE168945 | GEO
Project description:Purpose: The goal of this study is to determine whether hepatic deletion of Mettl3 affects chromatin accessibility. Methods: Liver samples were pooled from livers of Mettl3 HKO and Mettl3 flox/flox mice (n=4 for each group). Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol. Results: The hepatic chromatin accessibility in Mettl3 flox/flox and HKO mice were characterized.
2021-10-29 | GSE141245 | GEO
Project description:Alternative cleavage and polyadenylation (APA) is a form of transcriptional regulation via shifts in how frequently multiple polyadenylation (polyA) sites within genes are used across biological conditions. APA can result in transcripts with varying length and information content, and has been linked to gene regulation in both cancer and development. We performed a genome-wide quantification of polyA site usage using a next generation sequencing technique. By priming the polyA-tails of an RNA library, we mapped cleavage sites and abundances with base-pair resolution across the genomes of the DICER(ex5) hypomorph cells. The DICER cell line is derived from the parental HCT116 colon cancer cell line, but has an ablation of DICER function. This polyA sequencing data may be used to interrogate any cross-talk between DICER function and APA.
2022-12-29 | GSE86177 | GEO
Project description:Single-cell RNA sequencing methods based on split-pool combinatorial barcoding enable high-throughput profiling, yet sample identity is often encoded during early barcoding steps rather than through the library index. Consequently, reads from multiple biological samples remain pooled, complicating per-sample analysis and selective extraction of samples of interest. Here, I present CapMux, a Snakemake-based pipeline for processing split-pool scRNA-seq data from raw sequencing files to sample-resolved outputs. CapMux supports workflows starting from either BCL files or FASTQ files and reconstructs sample identity by integrating sub-library index information with the experiment-specific barcoding plate layout. The pipeline was developed for the CapSeq method but is configurable for related scRNA-seq combinatorial barcoding designs through specification of barcode positions and experimental layout. CapMux resolves pooled data into outputs for each sample, enabling independent quality control summaries, mapping statistics, count matrices, and downstream visualizations. Runtime benchmarking indicated that secondary demultiplexing step added only a modest computational overhead. Together, these results show that CapMux provides a practical and adaptable framework for recovering sample-level resolution from split-pool scRNA-seq data.
2026-03-19 | GSE324486 | GEO
Project description:Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.
2023-03-18 | GSE198863 | GEO
Project description:Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.
2023-09-06 | GSE198893 | GEO