|
Status |
Public on Nov 14, 2018 |
Title |
WT_V8_24h_2 |
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: 24h
|
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.
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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, 24h 24h.2
|
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of genes (DEGs) was assessed using DEseq2 v1.16.1 of R package Please note that the C. neoformans xl280 genome (unpublished) was used for mapping, but the mapping results are presented with the JEC21 homolog.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
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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 |
SAMN08725512 |
SRA |
SRX3805159 |