|
| Status |
Public on Oct 18, 2022 |
| Title |
bzp4, LIT, rep3 [bzp4_LIT_2hr_3] |
| Sample type |
SRA |
| |
|
| Source name |
H99
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
cell line: H99
cell type: Fungi
genotype: bzp4 knockout
treatment: capsule-inducing condition
|
| Treatment protocol |
Half of the cells were further incubated in an LIT liquid medium for 2hr
|
| Growth protocol |
Cryptococcus neoformans strains were grown at 30°C for 16hr in a YPD medium and transferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Then the cells were harvested by centrifugation and lyophilized. Total RNAs were prepared as described above and purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent). Cultured samples were prepared independently three times, and the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by the Illumina platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of C. neoformans H99 and annotation data were downloaded from the NCBI FTP server, derived from Broad Insitute.
The reads were aligned to the C. neoformans H99 genome sequence using Hisat2 v2.2.1 with the HISAT and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30” and “– dta -1” options and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with the “-Sb -@ 8” option for converting, and “-@ 20 –m 2000000000” option for sorting, and the other parameters were set as default.
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using the “-p 12” option, and also the “-B” option to run the Ballgown analysis. Assembled transcripts were merged to a single GTF file, and the relative transcript abundances were calculated via Fragments Per Kilobase of exon per Million fragments mapped (FPKM). The FPKM and read count matrix were generated by the R package “isoformswitchanalyzerR” and analyzed by DESeq2. Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown
The volcano plot was illustrated by using R v4.1.0 and R package "EnhancedVolcano", with the cutoff (more than two-fold changes with p< 0.05). PCA plot was generated by R package "DeBrowser" and heatmap was also generated by following R package
KEGG pathway analysis was performed using the R package "Cluster profiler", after changing H99S gene locus ID to JEC21 orthologue locus ID.
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Oct 18, 2022 |
| Contact name |
Yong-Sun Bahn |
| E-mail(s) |
ysbahn@yonsei.ac.kr
|
| Phone |
010-9971-9056
|
| Organization name |
Yonsei university
|
| Department |
Department of Biotechnology
|
| Lab |
Microbial Biotechnology Laboratory
|
| Street address |
50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL32481 |
| Series (1) |
| GSE208163 |
Unraveling capsule biosynthesis and signaling networks in Cryptococcus neoformans |
|
| Relations |
| BioSample |
SAMN29721297 |
| SRA |
SRX16208030 |
