|
| Status |
Public on Jan 21, 2020 |
| Title |
RNA whole body NE579 37S rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Cryptococcus neoformans var. neoformans |
| Characteristics |
strain: NE579 upf1delta
growth condition: exponential phase 30 degrees C
protocol: RNA-Seq
sample id: Sample 27
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C genomes with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). RNA Reads count were evaluated using HTSeq/0.6.1 (intersection-nonempty) normalized using the S. cerevisiae DNA/RNA spike in alpha factor and used to calculate FPKM values.
|
| |
|
| Submission date |
Jul 02, 2019 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Guilhem Janbon |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Pasteur
|
| Street address |
25 rue du Dr Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL26812 |
| Series (1) |
| GSE133695 |
Transcriptome of Cryptococcus neoformans and Cryptococcus deneoformans |
|
| Relations |
| BioSample |
SAMN12187149 |
| SRA |
SRX6389236 |
