BATSeq of ESC-FCS/ESC-2i/NSC
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE60768 | GEO | 2015/06/09
SECONDARY ACCESSION(S): PRJNA259519
REPOSITORIES: GEO
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Project description:Single-cell polyadenylation site quantification 48 single cells each of murine embryonic stem cells maintained in FCS+LIF medium ("ESC"), embryonic stem cells maintained in serum free, 2i containing medium ("2i") and neural stem cells ("NSC") were sequenced by BATSeq, a single cell transcriptomic protocol for mapping polyadenylation sites in single cells.
2015-06-09 | E-GEOD-60768 | biostudies-arrayexpress
Project description:Prevailing poly(dT)-primed 3’ single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site, which is expected to be the poly(A) tail or a genomic adenine homopolymer. Direct sequencing across this priming site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the ‘barcode’ end. Here, we evaluate the capability of “avidity base chemistry” DNA sequencing from Element Biosciences to sequence through this homopolymer accurately, and the impact of the additional cDNA sequence on read alignment and precise quantification of polyadenylation site usage. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy.
2024-07-30 | GSE273222 | GEO
Project description:Alternative polyadenylation (APA) plays an important role in post-transcriptional gene regulation. But how genes' APA usages are influenced by cell cycle remains largely unknown. Here we developed single cell polyadenylation sequencing (scPolyA-seq), a strand-specific approach for sequencing 3’ end of transcripts which can get very deep sequencing level around polyA site for each cell, to investigate the landscape of APA at single cell level, based on Fluidigm C1. We compared APA changes before and after thymidine double blocking (TdR) synchronization of HeLa cells. We then identify 6 gene clusters whose distal polyA site usages fluctuate during cell cycle.
2021-06-16 | GSE178264 | GEO
Project description:Direct-RNA Sequencing expression data, quantifying both abundance and 3'-processing (cleavage and polyadenylation) site was obtained for two distinct mutations of Pcf11 and matched wildtype w303 samples under both standard growth conditions, as well as under growth in a caffeine-supplemented medium, since these mutations have been shown to increase susceptiblity to caffeine-related phenotypes. The overall goal was quantification of expression and pre-mRNA processing changes in response to these mutations.
2023-11-01 | GSE190050 | GEO
Project description:The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939. The whole-genome microarray analyses is performed to confirm the identity of EpiSC maintained in CHIR/XAV by comparing the expression profile in EpiSC-CHIR/XAV to those in ESC maintained in 2i and EpiSC maintained in FGF2/activin.
2011-08-19 | GSE31461 | 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:FCS and MCM appear highly similar disorders. However, they importantly differ in term of risk and response to treatments. Some sets of genes might be up or down regulated in both disorders and could partly explain those differences. We used microarrays to explore gene expression patterns in FCS and MCM patients to identify potential targets that can be selected for protein quantification and functional studies.
2020-05-08 | GSE149607 | GEO
Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae. Experimental benchmark of five different protocols (3tfill, bpmI, internal, rnaseq and yoon) for genome-wide identification of polyadenylation sites in Saccharomyces cerevisiae and transcript quantification. RNA was extracted from WT cells grown in glucose (ypd) or galactose (ypgal) as carbon source. The same RNA was used for 3 independent library constructions (technical replicates, rep).
2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress
Project description:Purpose: Quiescence is a state of reversible cell cycle exit. Levels of polyadenylation factors decreases when proliferating cells become quiescent. The goals of this study are to determine the differential use of polyadenylation sites (changes in alternative polyadenylation) in quiescent vs. proliferating cells and also upon knockdown of polyadenylation factors. Methods: Two biological replicates of human dermal fibroblasts (12-1 and 12-3) were used for polyadeylation-site enriched RNA-seq on an Illumina HiSeq 2500 to compare quiescent vs. proliferating cells and polyadenylation factor knockdown vs. control cells. The reads were aligned to the human genome (hg19) uisng Tophat (2.0.14). The resulting bam files were used as an input to a python script provided by Gruber et al. (PMID: 27382025) to determine the counts for each polyadenylation site. Results: We observed a shift toward greater use of distal polyadenylation sites when the fibroblasts entered quiescence. We observed significant overlap between the genes that shift to greater distal site use with quiescence and CstF-64 or CPSF73 knockdown. Conclusions: The shift to greater distal site use with quiescence may reflect in part the reduced levels of cleavage and polyadenylation factors.
2018-08-28 | GSE117033 | GEO