|
| Status |
Public on May 29, 2024 |
| Title |
Sm_NecHi_Log_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cell
|
| Organism |
Serratia marcescens |
| Characteristics |
strain: PIC3611
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 |
Sm_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 |
GPL34520 |
| Series (1) |
| GSE268149 |
Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation |
|
| Relations |
| BioSample |
SAMN41494779 |
| SRA |
SRX24655151 |
