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| Status |
Public on Nov 11, 2022 |
| Title |
2nd ktr3Δcap6Δ_Tunicamycin |
| Sample type |
SRA |
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| Source name |
yeast
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| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: ktr3{delta}cap6{delta}
genotype: MAT{alpha}Cn03832::NAT#159 Cn06016::NEO
treatment: Tunicamycin
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| Treatment protocol |
The cells were then treated with 5 ug/ml tunicamycin (TM) and further incubated at 30°C in a shaking incubator for 1 h.
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| Growth protocol |
WT and mutant strains cells at OD600 (optical density at 600 nm) = 0.15 were cultured into 50 ml of YPD broth at 30°C in a shaking incubator until the OD600 reached 0.8, which is nearly the early phase of exponential growth.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The cell pellets were washed with diethyl pyrocarbonate (DEPC)-treated water twice, immediately frozen in liquid nitrogen, and disrupted thoroughly using a mortar and pestle. Total RNAs were extracted using the RNeasy Mini Kit (Qiagen
For RNA-sequencing, the NEBNext Ultra Ⅱ Directional RNA-Seq Kit (NEW ENGLAND BioLabs) was used to prepare libraries. The mRNA was isolated by using the Poly(A) RNA Selection Kit (LEXOGEN) and isolated mRNAs were used for the cDNA synthesis. The Illumina indexes 1–12 were used to perform indexing and enrichment step was carried out.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
none
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| Data processing |
To perform high-throughput sequencing as paired-end 100 sequencing, NovaSeq 6000 (Illumina) was used.
The raw sequencing data was checked quality control using the FastQC. FASTX_Trimmer and BBMap were used to remove adapter and low-quality reads (<Q20), then the TopHat was used to map the trimmed reads with reference genome.
Gene expression levels were estimated using FPKM (fragments per kb per million reads) values, which normalized using EdgeR within R.
RNA-seq analysis was conducted using the ExDEGA (ebiogen).
Assembly: Cryptococcus neoformans var. grubii H99 (assembly CNA3)
Supplementary files format and content: mRNA-seq_Report_gene_processed data files 1/2:
mRNA-seq_Report_gene_processed data file 1 - sample comparison in replication case (Group comparison 1: H99-plus/ H99-minus, Group comparison 2: KC-plus/ KC-minus)
mRNA-seq_Report_gene_processed data file 2 - sample comparison in no replication case (comparison 1: H99-plus/ H99-minus, comparison 2: 1stKC-plus/ 1stKC-minus, comparison 3: 1stKC-minus/ 1stH99-minus, comparison 4: 2ndH99-plus/ 2ndH99-minus, comparison 5: 2ndKC-plus/ 2ndKC-minus, comparison 6: 2ndKC-minus/ 2ndH99-minus, comparison 7: 2ndH99-minus/ 1stH99-minus, comparison 8: 2ndH99-plus/ 1stH99-plus, comparison 9: 2ndKC-minus/ 1stKC-minus, comparison 10: 2ndKC-plus/ 1stKC-plus)
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| Submission date |
Mar 17, 2022 |
| Last update date |
Nov 11, 2022 |
| Contact name |
EunJung Thak |
| E-mail(s) |
[email protected]
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| Phone |
(984) 837-0769
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| Organization name |
eunjungthak
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| Street address |
2530 erwin rd
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| City |
Durham |
| ZIP/Postal code |
27705 |
| Country |
USA |
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| Platform ID |
GPL28713 |
| Series (1) |
| GSE198875 |
Extension of O-linked mannosylation in the Golgi is critical for cell wall integrity signaling and interaction with host cells in Cryptococcus neoformans pathogenesis |
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| Relations |
| BioSample |
SAMN26750186 |
| SRA |
SRX14495031 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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