|
| Status |
Public on Nov 14, 2018 |
| Title |
WT_V8_72h_1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Cryptococcus neoformans var. neoformans XL280 |
| Characteristics |
strain: Cryptococcus neoformans var. neoformans serotype D XL280 MATalpha
genotype: wild type
time: 72h
|
| Treatment protocol |
Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.
|
| Growth protocol |
50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25℃ in dark.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar) at 25°C, 72h
72h.1
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to JEC21α whole genome using Hisat2 v2.1.0 with parameters hisat -p -x -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (TPM) were calculated using Stingtie v1.3.3 with parameters stringtie -p -e -G -o -A-C
The differential expression of genes (DEGs) was assessed using DEseq2 v1.16.1 of R package
Please note that the C. neoformans xl280 genome (unpublished) was used for mapping, but the mapping results are presented with the JEC21 homolog.
Genome_build: JEC21α
Supplementary_files_format_and_content: TPM values for each Sample
|
| |
|
| Submission date |
Mar 17, 2018 |
| Last update date |
Nov 14, 2018 |
| Contact name |
lei chen |
| E-mail(s) |
threestonechen@outlook.com
|
| Phone |
18066336645
|
| Organization name |
the institute of microbiology chinese academy of sciences
|
| Street address |
NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL24742 |
| Series (1) |
| GSE111975 |
Genetic basis for coordination of meiosis and sexual structure maturation in Cryptococcus neoformans |
|
| Relations |
| BioSample |
SAMN08725509 |
| SRA |
SRX3805162 |
