|
| Status |
Public on Jan 21, 2020 |
| Title |
PAS whole body KN99alpha 37E rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: KN99alpha
growth condition: exponential phase 37 degrees C
protocol: QuantSeq 3-prime RNA-Seq
sample id: Sample 6
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were grown on YPD at 37°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. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 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 |
QuantSeq 3’mRNA-Seq reads containing both the Sequencing and indexing primers (Lexogen) were sorted. The reads were then cleaned using cutadapt/1.18 and trimmed for polyA sequence in their 3’end. PolyA untrimmed and trimmed reads were mapped to the adapted Cryptococcus neoformans H99 genome with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). To eliminate the polyadenylated reads corresponding to genomic polyA stretches, we considered only the reads that aligned to the genomes only after polyA trimming. The 3’end position of these reads were considered as potential PAS. Wig files were constructed using the 3’ extremities of these reads Their coverage was normalized using the normalization alpha factor used for spiked in RNA-Seq.
|
| |
|
| 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 |
GPL19081 |
| Series (1) |
| GSE133695 |
Transcriptome of Cryptococcus neoformans and Cryptococcus deneoformans |
|
| Relations |
| BioSample |
SAMN12187075 |
| SRA |
SRX6389154 |
