|
| Status |
Public on Apr 11, 2017 |
| Title |
Treated mutant |
| Sample type |
SRA |
| |
|
| Source name |
mazEF mutant
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
strain: R1
genotype/variation: mazEF mutant
treated with: 15 μg/ml MMC for 30 min
|
| Treatment protocol |
D.radiodurans wild-type and ΔmazEF-dr cells were grown to OD600 of 0.6, and then each culture was divided in half; one half was treated with a sub-lethal MMC (15 μg/ml for 30 min) and the other untreated half was used as a control.
|
| Growth protocol |
D. radiodurans strains were grown in TGY media and 10 µg/ml Streptomycin was used for the mutant strain.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol method. Then, Dnase I was used to digest the DNA and Ribo-Zero Magnetic Kit was used to remove the rRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R1 whole genome using Rockhopper 1.20 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Deinococcus radiodurans R1; ASM856v1
Supplementary_files_format_and_content: RPKM values
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Li |
| E-mail(s) |
[email protected]
|
| Phone |
18667166273
|
| Organization name |
zhejiang university
|
| Department |
Institute of Nuclear-Agricultural Sciences
|
| Lab |
Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province
|
| Street address |
Kaixuan road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310000 |
| Country |
China |
| |
|
| Platform ID |
GPL23271 |
| Series (1) |
| GSE97563 |
RNA-seqanalysis of deinococcus wild-type and mazEF mutant strains after MMC treatment |
|
| Relations |
| BioSample |
SAMN06703832 |
| SRA |
SRX2731651 |
