|
| Status |
Public on May 29, 2021 |
| Title |
ReCrzA-3 |
| Sample type |
SRA |
| |
|
| Source name |
CrzA recover strain in glucose
|
| Organism |
Penicillium oxalicum |
| Characteristics |
strain: CrzA recover strain
medium: Modified Mendal’s medium with 2% starch as carbon resource
culture time: 18h after transferring washed mycelia to the new medium
tissue: Fungal mycelia
|
| Growth protocol |
The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% strach as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% strach as carbon resources for 18h. Total RNA was extracted for DGE analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 28, 2021 |
| Last update date |
May 29, 2021 |
| Contact name |
Kaili Zhao |
| E-mail(s) |
zhaokaili@mail.sdu.edu.cn
|
| Organization name |
ShanDong University
|
| Street address |
National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road
|
| City |
QingDao |
| ZIP/Postal code |
266237 |
| Country |
China |
| |
|
| Platform ID |
GPL24231 |
| Series (1) |
| GSE175771 |
Transcription factor CrzA modulate fungal development and cellulolytic gene expression in Penicillium oxalicum |
|
| Relations |
| BioSample |
SAMN19413911 |
| SRA |
SRX11018851 |
