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| Status |
Public on Apr 17, 2023 |
| Title |
CCB1244 (pXsa-t15-r3) |
| Sample type |
SRA |
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| Source name |
Bacterial cell
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| Organism |
Bacillus subtilis |
| Characteristics |
cell type: Bacterial cell
genotype: [delta]roxS, amyE::pXsa
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| Growth protocol |
Strains CCB1244 and CCB1243 were grown in 50 ml MD modified supplemented with 0.5 % malate and a limiting concentration of lysine (85.5 µM) with shaking at 37°C. Cultures were grown to OD600 = 0.5 and split in two cultures of 20 mL (For RNaseq and Pulsed SILAc experiment). For the RNaseq sample, 1 % arabinose was added for 15 min before harvesting the cultures (10 mL) for RNAseq
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 10 mL culture (pelleted and frozen) by the glass beads/phenol method described previously (Bechhofer DH et al. 2008, Methods Enzymol 447:259–276.). RNA samples were treated with RQ DNase Promega (37°C for 20 min) to remove potential contaminating chromosomal DNA. Ribosomal RNA was removed using the RiboZero kit (Illumina), and ribosomal RNA depletion and overall RNA quality was analysed by Bioanalyser (Agilent).
cDNA libraries were prepared using the Smarter Stranded RNA-Seq Kit (Clontech) with adapters for multiplexing, according to the manufacturer’s instructions. cDNA concentration and quality were checked by Bioanalyser (Agilent). The 6 samples were normalised to 2 nM, multiplexed and denatured at a concentration of 1 nM using 0.1 N NaOH (5 min at room temperature) before dilution to 10 pM and loading on a HiSeq Rapid SE65
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality control checks were performed before and after trimming by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Fifty-nt reads were mapped by Bowtie (Langmead et al, 2009)
The analysis is performed using the R [R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2013.] software, Bioconductor [R.-C. Gentleman and others. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, 5:R80, 2004.] packages including DESeq2.
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2 and the PF2tools package (version 1.5.3) developed at PF2 (Institut Pasteur)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Apr 11, 2023 |
| Last update date |
Apr 17, 2023 |
| Contact name |
Sylvain Durand |
| Organization name |
CNRS
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| Department |
UMR8261
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| Lab |
RNAmad
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| Street address |
13 rue Pierre et Marie Curie
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL19910 |
| Series (1) |
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| Relations |
| SRA |
SRX19933995 |
| BioSample |
SAMN34145710 |
| 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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