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| Status |
Public on Dec 20, 2019 |
| Title |
GM_2 |
| Sample type |
SRA |
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| Source name |
Fermentation mixture
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| Organism |
Komagataella phaffii |
| Characteristics |
strain: Komagataella phaffii GS115
fermentation stage: Glycerol and methanol mixture feed culture at 2 h
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| Growth protocol |
High-cell-density fed-batch cultivation encompassing four stages, namely, bench-scale batch fermentation, glycerol feed, GM phase, and methanol induction phases is used for Pichia pastoris to analysis the synthesis of recombinant proteins and investigating responses to various carbon sources
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| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GM_2
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| Data processing |
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GS115 whole genome using Hisat2 v2.0.5
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.The effect of sequencing depth and gene length on fragments count was also considered.
Genome_build: GS115
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Dec 19, 2019 |
| Last update date |
Dec 22, 2019 |
| Contact name |
Zunxi Huang |
| E-mail(s) |
bosmn@126.com
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| Organization name |
Yunnan Normal University
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| Street address |
768 Ju Xian Street
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| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650500 |
| Country |
China |
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| Platform ID |
GPL27930 |
| Series (1) |
| GSE142326 |
Transcriptomic analysis of Pichia pastoris (Komagataella phaffii) GS115 during heterologous protein production using a high-cell-density fed-batch cultivation strategy |
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| Relations |
| BioSample |
SAMN13633024 |
| SRA |
SRX7415646 |
| 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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