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Sample GSM7937422 Query DataSets for GSM7937422
Status Public on Dec 05, 2023
Title byMM1827
Sample type SRA
 
Source name experimental strain contains denAsCas12a:ScRNA activator for HED1 endogenous gene activation
Organism Saccharomyces cerevisiae
Characteristics cell type: eukaryocyte
genotype: MATa; his3D1; leu2-3_112; ura3-52; trp1-289; MAL2-8c; SUC2
treatment: Experimental strain included denAsCas12a, MCP-VP64 fusion protein, ScRNA that can target to pHED1, the final result was activate the expression of HED1 endogenous gene.
Extracted molecule total RNA
Extraction protocol toal RNA was ectracted and quality from S. cereviase by using Total RNA Extractor (Trizol) and Qubit2.0 RNA examination kit
Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
Data processing Data evaluation and quality control: 1) The quality of the original data of sequencing was evaluated by FastQC. 2) Trimmomatic is used for mass shearing, and relatively accurate and effective data are obtained.
RNAseq sequencing evaluation: 1) Compare the valid data of the sample with the reference genome by using HISAT2, and count the Mapping information. 2) According to the comparison results, RSeQC was used to perform redundant sequence analysis and insert fragment distribution analysis. 3) Using Qualimap to check the homogeneity distribution and analyze the genome structure distribution according to the comparison results. 4) statistical analysis of gene coverage and distribution of sequencing sequences on chromosomes were carried out by BEDTools.
Gene structure analysis: 1) Use BCFtools to find out possible SNP sites according to the Mapping results, and use SnpEff to determine the influence of SNP sites on genes. 2) Assemble the sequence Mapping to the genome with StringTie, and then compare it with the known gene model with GffCompare to find new transcription regions. 3) Perform variable shear analysis with ASprofier. 4) Use EricScript to analyze the fusion gene.
Expression level analysis: 1) Use StringTie and known gene models to evaluate the expression of genes. 2) Using WGCNA to analyze the co-expression of genes. 3) Multi-directional statistical analysis and exploration, such as comparative analysis of samples, are carried out based on the expression matrix of samples.
Analysis of expression differences: 1) Use DESeq2 to analyze gene expression difference, and visualize the results of expression difference analysis. 2) Mapping the differential genes to the STRING protein interaction network database to construct the protein interaction network. 3) Based on the results of difference analysis, Wayne diagram and heat map are drawn and cluster analysis is carried out.
Assembly: Saccharomyces cerevisiae S288C(NCBI)
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1777 and byMM1827), log 2 fold changes, P-value, Q- value, results
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1736 and byMM1832), log 2 fold changes, P-value, Q- value, results
 
Submission date Dec 05, 2023
Last update date Dec 05, 2023
Contact name Lifang Li Yu
E-mail(s) msylf@tju.edu.cn
Phone 15222137152
Organization name Tianjin University
Street address Wei Jin road
City Tianjin
State/province Tianjin
ZIP/Postal code 678351
Country China
 
Platform ID GPL33987
Series (1)
GSE249355 Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.
Relations
BioSample SAMN38670426
SRA SRX22768419

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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