|
| Status |
Public on Jan 21, 2020 |
| Title |
DNA 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: DNA-Seq
sample id: Sample 27
|
| Extracted molecule |
genomic DNA |
| 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 DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
alpha_factor.txt
|
| Data processing |
Library strategy: DNA-Seq
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 Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor. The file with the alpha noramlization factors is available on the series record: alpha_factor.txt
|
| |
|
| Submission date |
Jul 02, 2019 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Guilhem Janbon |
| E-mail(s) |
janbon@pasteur.fr
|
| 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 |
SAMN12187150 |
| SRA |
SRX6389235 |
