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| Status |
Public on Sep 15, 2024 |
| Title |
Neurospora crassa Crf4-3 mutant, Control, rep 3 |
| Sample type |
SRA |
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| Source name |
mycelia
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| Organism |
Neurospora crassa |
| Characteristics |
tissue: mycelia
genotype: Crf4-3 knockout
treatment: No treatment
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| Treatment protocol |
Ketoconazole (Sigma) was added, with final concentration of 1.5 μg/mL.
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| Growth protocol |
Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors 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 |
DNBSEQ-T7 |
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| Description |
C3_84KO
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| Data processing |
Basecalling was performed using a software developed for DNBSEQ-T7.
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.
Assembly: 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 |
Jul 13, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
pengju YU |
| E-mail(s) |
pengju195@outlook.com
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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 |
GPL31176 |
| Series (1) |
| GSE272185 |
A PWWP domain-containing protein Crf4-3 specifically modulates fungal azole susceptibility by regulating sterol C-14 demethylase ERG11 |
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| Relations |
| BioSample |
SAMN42483732 |
| SRA |
SRX25318174 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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