|
| Status |
Public on May 04, 2018 |
| Title |
WU-2 |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
strain: R1
genotype: wild type
protocol: under normal conditions
|
| Treatment protocol |
For treated group, Cells were incubated to an OD600 of approximately 0.8, centrifuged and resuspended in phosphate buffer, then treated with 100 mM H2O2 for 30 minutes.
|
| Growth protocol |
D. radiodurans R1 and its derivatives were grown at 30°C in TGY broth (0.5% tryptone, 0.1% glucose, and 0.3% yeast extract).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 4 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
under normal conditions
|
| Data processing |
Illumina Casava1.8.2 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 soap maximum number of mismatches allowed = 2bp， number of valid alignments per read pair (-k) = 40
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans_R1_uid57665
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lin Lin |
| E-mail(s) |
[email protected]
|
| Phone |
+86-571-86971215
|
| Organization name |
Zhejiang University
|
| Department |
Institute of Nuclear-Agricultural Sciences
|
| Street address |
No.268, Kaixuan Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310029 |
| Country |
China |
| |
|
| Platform ID |
GPL19650 |
| Series (1) |
| GSE68494 |
RNA-seq-based Transcriptome Analysis of A LuxR-like (DqsR) Mutant of Deinococcus radiodurans Under Oxidative and Non-oxidative Stresses. |
|
| Relations |
| BioSample |
SAMN03580811 |
| SRA |
SRX1016226 |
