|
| Status |
Public on Feb 16, 2020 |
| Title |
wild type that treated iron (sample 3) |
| Sample type |
SRA |
| |
|
| Source name |
WT-H-3
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
genotype: wild type
culture condition: YNB low iron medium + 100 μM of FeCl3
|
| Growth protocol |
C. neoformans cells were cultured in YNB + BPS with or without 100 μM of FeCl3 at 30˚C for 6 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RiboPure-Yeast Kit (Ambion, #AM1926) following manufacturer's instructions.
Library was constructed using Illumina TruSeq RNA Library Prep Kit V2 following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
wild type that treated iron (sample 3)
|
| Data processing |
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, normalization of retrieved counts and fold change calculation between groups were performed by DESeq2 package.
Genome_build: C. neoformans var. grubii H99 (GCA_000149245.3)
Supplementary_files_format_and_content: Normalized counts, fold change values and related p-values were listed as a xlsx format for each sample.
|
| |
|
| Submission date |
Feb 08, 2019 |
| Last update date |
Feb 16, 2020 |
| Contact name |
Yong-Joon Cho |
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21548 |
| Series (2) |
| GSE126313 |
Transcriptome analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability |
| GSE126314 |
ChIP-Seq and RNA-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability |
|
| Relations |
| BioSample |
SAMN10900587 |
| SRA |
SRX5353062 |
