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| Status |
Public on Jul 12, 2023 |
| Title |
CY-3day-01 miRNA-Seq |
| Sample type |
SRA |
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| Source name |
whole cells
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| Organisms |
Auxenochlorella pyrenoidosa; Yarrowia lipolytica |
| Characteristics |
cell type: whole cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from C. pyrenoidesa and the co-culture system using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) with the manufacturer’s protocol.
The mRNA sequencing libraries were generated using the NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), and the miRNA sequencing library was generated using the Next Ultra-small RNA Sample Library Prep Kit for Illumina (NEB, USA)
miRNA-Seq、mRNA-Seq
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CY-3day-01
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| Data processing |
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC, including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database,Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files
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| Submission date |
May 01, 2023 |
| Last update date |
Jul 12, 2023 |
| Contact name |
Danni Lin |
| Organization name |
Zhongkai University of Agriculture and Engineering
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| Street address |
388 Guangxin Road, Baiyun District
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| City |
Guangzhou |
| ZIP/Postal code |
510550 |
| Country |
China |
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| Platform ID |
GPL33366 |
| Series (1) |
| GSE231399 |
Enhanced nitrogen removal via Yarrowia lipolytica-mediated nitrogen and related metabolism of Chlorella pyrenoidosa from wastewater |
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| Relations |
| BioSample |
SAMN34504582 |
| SRA |
SRX20174667 |
| 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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