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| Status |
Public on Oct 27, 2021 |
| Title |
IP-GY18220-rep3 |
| Sample type |
SRA |
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| Source name |
IP-GY18220-rep3
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| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
strain: ATCC13939
genotype: ddrO::v5
treatment: none
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| Treatment protocol |
For RNAseq samples : cells were grown at 37°C at indicated times for each samples
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| Growth protocol |
D. radiodurans cells were grown at 30°C in TGY2X (1% tryptone, 0.2% dextrose, 0.6% yeast extract)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP seq samples: cells were cross-linked with 1% formaldehyde in TGY2X medium for 25 min at 30°C with continuous shaking. Crosslinking reactions were quenched by the addition of 125 mM glycine for 15 min. Cells were harvested by centrifugation (4000 rpm, 10min, 4°C), washed twice with cold Tris Buffer Solution (TBS) and then resuspended in 3 mL of lysis buffer [160 nM NaCl, 20 mM, Tris-HCl pH7.5, 1 mM EDTA, protease inhibitor cocktail (Roche)]. Cells were disrupted and DNA sheared using a One Shot Cell Disruptor (CellD SARL) to an average size of 100-300 bp (2 rounds of 2.4kbar). Insoluble material was removed by centrifugation at 15,000 rpm for 10 min at 4°C and the supernatant was collected in a sterile microcentrifuge tube. Then, 500 µL of supernatant fluid was added to 25 µL of pre-incubated protein G magnetic beads (ChIP-Adembeads ChIP-Adem-Kit, Ademtech SA) with 5 µg of anti-V5 rabbit polyclonal antibody (ab9116, Abcam) in IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton 100, protease inhibitor cocktail (Roche)]. After overnight incubation at 4°C with rotation, the immunoprecipitates were washed 5 times with washing buffers (ChIP-Adembeads ChIP-Adem-Kit, Ademtech SA). Immune complexes were eluted in 200 µL of elution buffer. 20 µL The eluted samples (20µL) were saved for control Western blots, and the remainder was incubated for 2 h at 37°C with shaking with 100 µg/mL Proteinase K. Then, the supernatant was incubated overnight at 65°C to reverse cross-linking with 100 µg/mL RNAse A. The DNA was purified using the PCR Clean-up kit (Macherey-Nagel).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ddrO::v5
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| 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
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| Submission date |
Jun 01, 2021 |
| Last update date |
Oct 27, 2021 |
| Contact name |
Fabrice Confalonieri |
| E-mail(s) |
[email protected]
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| Phone |
33-1-0169156234
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| Organization name |
Institute for Integrative Biology of the Cell (I2BC)
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| Department |
Genome Biology
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| Lab |
Radioresistance of bacteria and archaea
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| Street address |
Avenue de la Terrasse
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| City |
Gif sur Yvette |
| ZIP/Postal code |
91198 |
| Country |
France |
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| Platform ID |
GPL30214 |
| Series (1) |
| GSE175875 |
Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses. |
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| Relations |
| BioSample |
SAMN19486400 |
| SRA |
SRX11036551 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5350261_IP-GY-18220-3_S13_all.genomeCoverage.bed.txt.gz |
9.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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