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| Status |
Public on Sep 01, 2023 |
| Title |
UT3 |
| Sample type |
SRA |
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| Source name |
prokaryotic cell
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| Organism |
Microcystis aeruginosa FACHB-905 = DIANCHI905 |
| Characteristics |
strain: FACHB-905 = DIANCHI905
cell type: prokaryotic cell
genotype: WT
treatment: Urea-N+PS-NH2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Urea-N+PS-NH2
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| Data processing |
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads need to be filtered by quality.
Trimmomatic software was first used for quality control and linker removal, and then low-quality bases and N-bases or low-quality reads were filtered out.
Finally, we got high-quality clean reads.
Using Rockhooper2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
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| Submission date |
Sep 30, 2022 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Mei-Yan Liu |
| E-mail(s) |
[email protected]
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| Phone |
15238377797
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| Organization name |
Shandong university
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| Street address |
Aoshanwei Street
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266000 |
| Country |
China |
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| Platform ID |
GPL32703 |
| Series (1) |
| GSE214536 |
Differentially forms of nitrogen regulates the response of Microcystis aeruginosa to nanoplastics under environmentally relevant nitrogen concentration |
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| Relations |
| BioSample |
SAMN31109208 |
| SRA |
SRX17764309 |
| 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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