|
| Status |
Public on Oct 27, 2021 |
| Title |
17370_16H-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
17370_16H-rep3
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
strain: ATCC13939
genotype: deltaddrO/ p:repUts::ddrO+
treatment: 37degreeC
time point: 16H
|
| Treatment protocol |
For RNAseq samples : cells were grown at 37°C at indicated times for each samples
|
| Growth protocol |
D. radiodurans cells were grown at 30°C in TGY2X (1% tryptone, 0.2% dextrose, 0.6% yeast extract)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNAseq samples : total RNA was isolated using the Fast RNA Pro Blue Kit (MP Biomedicals) and the FastPrep-24 instrument, according to the manufacturer’s protocols. Extracted RNA was rigorously treated with TURBO DNA-free (Invitrogen).
The rRNA depletion and Illumina libraries were made following the Illumina protocol (Script-Seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ΔddrO/ p:repUts::ddrO+
|
| Data processing |
The quality score was verified with FASTQC software and Illumina adaptor sequences were removed with Cutadapt software
For RNA-seq samples: Read sequences were mapped with BWA mem [v. 0.7.9a-r786] using default settings
For RNA-seq samples: coverage values of all genomic features were computed with the bedtools “coverage” command [v2.17.0]
For RNA-seq samples: RNA differential gene expression analysis was performed with the DESeq R-package [v. 1.39.0]
For ChIP-seq samples : Sequence alignments on the genomic sequence were performed with Bowtie2 software (default parameters)
For ChIP-seq samples : Output SAM files were converted and indexed into BAM files, using the Samtools software
For ChIP-seq samples: They were used for additional conversion into BED files with Bedtools software providing the input file format required by bPeaks programs to perform peak calling (bPeaks parameters: 2,2,0.5,0.9)
Genome_build: PRJNA684478
|
| |
|
| Submission date |
Jun 01, 2021 |
| Last update date |
Oct 27, 2021 |
| Contact name |
Fabrice Confalonieri |
| E-mail(s) |
[email protected]
|
| Phone |
33-1-0169156234
|
| Organization name |
Institute for Integrative Biology of the Cell (I2BC)
|
| Department |
Genome Biology
|
| Lab |
Radioresistance of bacteria and archaea
|
| Street address |
Avenue de la Terrasse
|
| City |
Gif sur Yvette |
| ZIP/Postal code |
91198 |
| Country |
France |
| |
|
| Platform ID |
GPL30214 |
| Series (1) |
| GSE175875 |
Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses. |
|
| Relations |
| BioSample |
SAMN19486390 |
| SRA |
SRX11036527 |
