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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 26, 2019 |
| Title |
21 |
| Sample type |
SRA |
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| Source name |
dac2Δ strain RNA-seq sample, replicate 1
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| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
genotype: dac2_delta
growth phase: logarithmic phase, OD600=1.0
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| Extracted molecule |
total RNA |
| Extraction protocol |
Transcriptome analysis: For the analysis of deacetylase inhibitors, C. neoformans cells were either not treated or treated with 3 μM TSA and 20 mM NAM in 50 ml of YPD medium at 30°C for 6 hrs. For the analysis of dac2Δ and dac4Δ, overnight cell cultures of the wild-type H99, dac2Δ and dac4Δ strains were subcultured in fresh YPD medium, and the cultures were incubated at 30°C until the cell density reached the exponential phase (approximately 6 to 7 hrs). Cells were then washed twice with ice-cold PBS supplemented with 3 μM TSA and 20 mM NAM, followed by RNA isolation using TRIzol reagent (Thermo Fisher Scientific, USA). Three micrograms of total RNA was processed using the TruSeq RNA sample preparation Kit (Illumina, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2
Software used for RPKM calculation: HTSeq 0.6.1p2
Software used for creation of the wig files: MACS
Genome_build: Cryptococcus neoformans var. grubii H99 .
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample (RNA-seq), wig files for ChIP-seq
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| Submission date |
Jun 20, 2018 |
| Last update date |
Apr 28, 2019 |
| Contact name |
Li Hailong |
| E-mail(s) |
lihailong1166@gmail.com
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| Organization name |
Northeastern University
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| Street address |
NO. 3-11, Wenhua Road, Heping District
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| City |
ShenYang |
| State/province |
Liaoning |
| ZIP/Postal code |
110001 |
| Country |
China |
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| Platform ID |
GPL24689 |
| Series (1) |
| GSE116040 |
Fungal acetylome comparative analysis identifies an essential role of acetylation in human fungal pathogen virulence |
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| Relations |
| BioSample |
SAMN09461758 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3207825_21.txt.gz |
88.3 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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