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| Status |
Public on Apr 28, 2023 |
| Title |
PoxCxrA-2 |
| Sample type |
SRA |
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| Source name |
HP7-1
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| Organism |
Penicillium oxalicum |
| Characteristics |
cell line: HP7-1
cell type: Mycelium
genotype: PoxCxrA knockout
treatment: Transfer from glucose medium to Avicel,and then culture for 24h
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| Growth protocol |
Fresh spores of the delta ku70 and mutant delta POX03070、delta PoxCxrA were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 4 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 10^8 spores per milliliter. The inoculated MMM containing glucose (1.0% w/v) with a final concentration of 1 × 10^6 spore/mL was pre-grown for 24 h at 28°C. The mycelia (~ 1.0 g) were collected and then transferred into fresh 100 mL liquid MMM containing 2% Avicel for 24 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using TRIzol RNA Kit
The total RNA is enriched, the RNA fragments are reverse transcribed with random N6 primers, and the cDNA obtained to synthesize double-stranded DNA. A sticky end of "A" is connected with a linker, the ligated product is amplified by PCR with specific primers, the PCR product is heat denatured to form a single-stranded DNA, and the single-stranded DNA is obtained by a bridge primer to obtain a single-stranded circularization library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Raw reads or raw data of the original sequencing sequence in FASTQ (fq) format are obtained after base calling and Bcl2 Fastq conversion.
The raw sequencing data contains linker information、low-quality bases、and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. Clean reads will be obtained after analyzing by SOAPnuke software (v2.1.0).
The clean reads mapped onto the genome of Penicillium oxalicum strain HP7-1 to functional annotation, using the software HISAT2
FPKM, representing gene expression levels, was calculated with the software RSEM.
Assembly: GenBank database under accession number JRVD02000000
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 23, 2022 |
| Last update date |
Apr 29, 2023 |
| Contact name |
Di Tian |
| E-mail(s) |
[email protected]
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| Phone |
18577787732
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| Organization name |
College of Life Science and Technology,GuangXi university
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| Street address |
DaXue east road
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| City |
Nanning |
| ZIP/Postal code |
530000 |
| Country |
China |
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| Platform ID |
GPL32390 |
| Series (1) |
| GSE206840 |
RNA-seq of mutant delta POX03070 and delta PoxCxrA after transfer from glucose medium to Avicel medium for 24 hours |
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| Relations |
| BioSample |
SAMN29272494 |
| SRA |
SRX15864141 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6265622_PoxCxrA-2_gene_fpkm.txt.gz |
53.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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