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Sample GSM8286400 Query DataSets for GSM8286400
Status Public on May 29, 2024
Title Cj_NecHi_Log_Rep2
Sample type SRA
 
Source name Bacterial cell
Organism Cellvibrio japonicus
Characteristics strain: Ueda107
cell type: Bacterial cell
genotype: WT
group: NecHi
growth phase: Log
Extracted molecule total RNA
Extraction protocol As per the protocol described in PMID: 22949721
Ribosomal RNA Depletion; RNA Fragmentation and Random Priming; Fist and Second Strand cDNA synthesis; End Repair with 5' phosphorylation and dA-Tailing; Adapter ligation with PCR enrichment; Sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description Cj_NecHi_TPM.csv
Necromass_DEG.xlsx
Data processing The raw FASTQ files were quality checked, aligned to existing genomes, and analyzed for differential expression using the Galaxy platform. Unless otherwise noted below, default parameters were in all analysis tools used except in cases where strandedness was specified (all RNAseq data were unstranded). Briefly, RNAseq data were concatenated using the concatenate data sets: tail-to-head (cat) tool. Transcript quality was tested using FastQC, which indicated read trimming was unnecessary for any of the files. Transcripts were next aligned to their respective reference genomes using the HISAT2 tool and quantified using the htseq-count tool. Reference genome files for C. japonicus Ueda107 (ASM1922v1) and C. pinensis DSM2588 (ASM2400v1) were obtained from ENSEMBLE, while that for S. marcescens PIC3611 was retrieved from NCBI Refseq (ASM2260299v1). Due to the differences in reference genome sources, the S. marcescens files required a parameter change in the htseq-count ‘feature type’ from ‘gene’ to ‘exon’. Differential gene expression using DESeq2 compared necromass exponential growth to necromass stationary phase for all three species and glucose for Cp and Sm.
Assembly: C. japonicus Ueda107 (ASM1922v1); C. pinensis DSM2588 (ASM2400v1); S. marcescens PIC3611 (ASM2260299v1)
Supplementary files format and content: TPM for biolgical repliates for a given substrate and bacterial species; DEG with p-values for pair-wise comparisons
 
Submission date May 22, 2024
Last update date May 29, 2024
Contact name Jeffrey G. Gardner
Organization name University of Maryland - Baltimore County
Department Department of Biological Sciences
Street address 1000 Hilltop Circle
City Baltimore
State/province MD
ZIP/Postal code 21250
Country USA
 
Platform ID GPL34518
Series (1)
GSE268149 Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation
Relations
BioSample SAMN41494816
SRA SRX24655109

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

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