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| Status |
Public on Mar 03, 2023 |
| Title |
Bacillus subtilis 168, Nutrient shift (Malate to Glucose) control - No Glucose, rep2 |
| Sample type |
SRA |
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| Source name |
Bacillus subtilis
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| Organism |
Bacillus subtilis |
| Characteristics |
strain: strain 168
cell type: Bacillus subtilis
treatment: Malate
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Total RNA Purification Kit (Norgen Biotek) according to maunfacturer's specifications for gram-positive bacteria
The rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented according to manufacturer’s instruction. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
M.Gcont.2
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| Data processing |
Nextflow nf-core/rnaseq 3.8.1
Trimming and removal of unwanted sequences by the following tools in the workflow: UMI-tools, Trim Galore 0.6.7, BBSplit, SortMeRNA
Alignment of reads performed by STAR 2.6.1d and quantified using Salmon 1.5.2
Additional FASTA file was included for alignment against ERCC spike-in controls, ERCC92
Assembly: eb2
Supplementary files format and content: tab-delimited text file containing a matrix of all gene-counts established by Salmon. Samples as columns, Features as rows.
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| Submission date |
Mar 03, 2023 |
| Last update date |
Mar 03, 2023 |
| Contact name |
David Markham |
| E-mail(s) |
d.markham2@newcastle.ac.uk
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| Organization name |
Newcastle University
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| Department |
ICOS
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| Street address |
Devonshire Building
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| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE1 7RU |
| Country |
United Kingdom |
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| Platform ID |
GPL30886 |
| Series (1) |
| GSE226559 |
RNA-seq established gene expression data to determine the effects of various stresses on Bacillus subtilis str.168 |
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| Relations |
| BioSample |
SAMN33577026 |
| SRA |
SRX19556218 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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