Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1002882 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We examined all transcriptome-level expressions in three initial cell-population densities (862, 1724 and 5172 cells/cm2) in the first two days of differentiation in N2B27. We collected cells in 10-mL tubes and centrifuged them using a pre-cooled centrifuge. We then extracted RNA from each cell-pellet using the PureLink RNA Mini Kit (Ambion, Life Technologies) according to its protocol. We next prepared the cDNA library with the 3′ mRNASeq library preparation kit (Quant-Seq, Lexogen) according to its protocol. We then loaded the cDNA library onto an Illumina MiSeq system using the MiSeq Reagent Kit v3 (Illumina) according to its protocol. We analyzed the resulting RNA-seq data as previously described (Trapnell et al., Nat Protoc 2012). We performed the read alignment using TopHat, read assembly using Cufflinks and analyses of differential gene expression data using Cuffdiff. We used the reference genome for Mus musculus from UCSC (mm10). We performed enrichment analysis of genes based on their FPKM values (e.g., more than 2-fold expressed when two initial population densities are compared) by using GO-terms from PANTHER (Mi et al., Nucl Acids Res 2019) and custom MATLAB script (MathWorks). We visualized results of pre-sorted, Yap1-related genes (LeBlanc et al., Elife 2018; Mugahid et al., Elife 2020; Yu et al., Oncogene 2018; Huh et al., Cells 2019; Zhu et al., Nature Sci Rep 2018; Zhou et al., Int J Mol Sci 2016; Vigneron & Vousden, EMBO J 2012; Kim et al., Cell 2015) into heat maps that displays the normalized expression value (row Z-score) for each gene and each condition.
2020-09-09 | GSE157642 | GEO
Project description:Comparison of leaves from potato grown in different fields during 2018 and 2019
2024-08-12 | PXD026690 | Pride
Project description:Purpose: Searching for sRNAs in Salmonella pullorum by RNA sequencing and exploring their functions.Methods: High-throughput sequencing of RNA extracted from Salmonella pullorum under normal growth conditions to detect newly discovered sRNAs, followed by experiments to verify their functions.Results: The proportion of Clean Reads of this sequencing was >65%, and the base Q30s were all above 85%, indicating that the sequencing quality is good and can be used for subsequent analysis. The sRNAscanner software predicted that 148 new sRNAs might exist on the reference genome of Salmonella fowl dysentery, and the reads obtained from sequencing were compared to the genome, and it was found that 110 out of the 148 newly predicted sRNAs could be detected.Conclusions: sRNAs are widely found in bacteria and are involved in many physiological processes. In this study, we detected new sRNAs in Salmonella pullorum by RNA-seq, which lays the foundation for the subsequent investigation of the regulatory functions of sRNAs in bacteria.
2024-06-10 | GSE269156 | GEO
Project description:In recent years, several small molecule cytotoxic drugs have been identified as potential inhibitors of ribosome biogenesis (Drygin et al., 2011; Peltonen et al., 2014a; Peltonen et al., 2014b). CX-5461 is one such drug that has also demonstrated anticancer potential for a wide range of malignancies (Bywater et al., 2012; Cornelison et al., 2017; Devlin et al., 2015; Drygin et al., 2011; Hald et al., 2019; Hein et al., 2017; Ismael et al., 2019; Lawrence et al., 2018; Lee et al., 2017; Negi and Brown, 2015; Taylor et al., 2019; Xu et al., 2017; Yan et al., 2017) (Haddach et al., 2012), and is presently under phase I trials for the treatment of both hematological cancers and solid tumours (Group, 2016; Khot et al., 2019). CX-5461 was initially characterized as an inhibitor of RNA Polymerase I (RPI/PolR1/PolI) that is responsible for the synthesis of the major ribosomal RNAs and the initial step in ribosome biogenesis (Drygin et al., 2011). Since RPI and its corresponding core transcription factors are dedicated to this task alone, they present ideal molecular targets by which to modulate ribosome biogenesis. However, the specificity of CX-5461 has been questioned and it has been suggested that this drug may also act by stabilizing DNA G-quadruplexes or by “poisoning” topoisomerase II (Topo II). Thus, the primary target of this drug and its mode of action are still in doubt. Here we used Deconvolution-ChIP-Seq in NIH3T3 and HEK293T cells treated for different times with CX-5461. The data show that the primary target of CX5461 is the initiation of ribosomal RNA gene (rDNA) transcription. CX-5461 blocks transcription initiation in vitro and in vivo by arresting RNA polymerase I (RPI/Pol1) within the preinitiation complex. In contrast to previous suggestions, CX-5461 does not effect recruitment of the TBP-TAF complex SL1 to the rDNA promoter, the recruitment of the initiation competent RPI-Rrn3 complex or ongoing transcription elongation, arguing against a role for G-quadruplex stabilization or topoisomerase II poisoning. Inhibition of transcription by CX-5461 is not reversible, the RPI-Rrn3 complex remains arrested in the preinitiation complex even after drug removal. This leads to nucleolar stress, extensive DNA damage and cell senescence. Our data show that the cytotoxicity of CX-5461 is the downstream result of the highly specific inhibition of rDNA transcription. The observation that this inhibition is irreversible will be important for the future design of chemotherapeutic strategies and the avoidance of drug resistance.
2021-04-07 | E-MTAB-9242 | biostudies-arrayexpress
Project description:Seif, 2019 - Systems biology and pangenome of Salmonella O-antigens
Strain-specific metabolic models of Salmonella strains updated with O-antigen metabolic pathways.
Locus-tags are updated in this version of the models to include both the prokka annotations and the refseq locus tags.
2019-09-11 | MODEL1907100002 | BioModels
Project description:Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) grown for 35 days on laminin-coated coverslips, a stiff matrix, were enzymatically dissociated, replated on laminin-coated coverslips and grown for further 2 days. Gene expression was compared with controls grown for 37 days on laminin-coated coverslips. Total RNA was isolated and gene expression was analyzed by RNA-sequencing (RNA-seq) on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Gene enrichment analysis based on RNA-Seq data of hESC-CMs replated for 2 days as compared with 37 days old controls was performed by using the comprehensive gene set enrichment analysis tool Enrichr for pathway analysis with KEGG Pathways 2019 Human, as well as for Gene Ontology (GO) analysis with GO Cellular Component 2018, GO Molecular Function 2018, and GO Biological Process 2018. Gene enrichment was also analyzed by Ingenuity Pathway analysis (IPA, Qiagen), especially Canonical Pathways analysis. Gene enrichment analysis revealed changes in the gene expression profile, especially of mechanosensation/-transduction-related genes and pathways in replated hESC-CMs.
2023-08-17 | GSE176154 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Genomic DNA from 191 asy1/+ Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Lawrence et al, 2019 Current Biology). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda); Yelina et al, 2015 Genes & Dev; Lawrence et al, 2019 Current Biology).
2020-05-18 | E-MTAB-8725 | biostudies-arrayexpress