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| Status |
Public on Jan 24, 2022 |
| Title |
WT rep1 |
| Sample type |
SRA |
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| Source name |
mycelium
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| Organism |
Neurospora crassa |
| Characteristics |
genotype: wild type
treatment: control (no treatment)
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| Treatment protocol |
Ketoconazole were added to a final concentration of 1 μg/mL
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| Growth protocol |
Briefly, 15 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 13 h and then treated with or without ketoconazole for 12 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
WT_1
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| Data processing |
Basecalling was performed using a software developed for BGISEQ-500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al., Genome Research, 1997.
Genome_build: GCA_000182925.2
Supplementary_files_format_and_content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.
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| Submission date |
Jan 19, 2022 |
| Last update date |
Jan 24, 2022 |
| Contact name |
Chengcheng Hu |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
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| Street address |
NO.1 Beichen West Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL29089 |
| Series (1) |
| GSE193984 |
Next Generation Sequencing Facilitates Quantitative Analysis of N. crassa Wild Type, stk-17ko and stk-17com Transcriptomes treated with or without ketoconazole |
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| Relations |
| BioSample |
SAMN25118862 |
| SRA |
SRX13830109 |
| 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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