NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8117653 Query DataSets for GSM8117653
Status Public on Dec 10, 2024
Title SA-9h, scRNA-seq, High sequencing depth results (0609-7)
Sample type SRA
 
Source name bacterial cell
Organism Staphylococcus aureus
Characteristics strain: ATCC 25923
cell type: bacterial cell
genotype: WT
treatment: stationary growth phase
Extracted molecule total RNA
Extraction protocol For RiboD-PETRI, all cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-PETRI, library was performed accarding to the Materials and Methods section;
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RiboD-PETRI
Detailed_Computational_Pipeline.txt
scripts.tar.gz
Data processing The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq datas were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples
 
Submission date Feb 28, 2024
Last update date Dec 10, 2024
Contact name Xiaodan Yan
E-mail(s) [email protected]
Phone 13283874287
Organization name Wuhan University
Department Medical Research Institute
Street address Donghu Road, No. 115, Wuchang District,
City Wuhan
State/province Hubei Province
ZIP/Postal code 430071
Country China
 
Platform ID GPL27158
Series (2)
GSE260457 An Improved Bacterial Single-cell RNA-seq Reveals Biofilm Heterogeneity [scRNA-seq]
GSE260458 An Improved Bacterial Single-cell RNA-seq Reveals Biofilm Heterogeneity
Relations
BioSample SAMN40188188
SRA SRX23779280

Supplementary file Size Download File type/resource
GSM8117653_Table-S14.Matrix_of_SA_data.txt.gz 2.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap