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Sample GSM6610937 Query DataSets for GSM6610937
Status Public on Sep 01, 2023
Title NT2
Sample type SRA
 
Source name prokaryotic cell
Organism Microcystis aeruginosa FACHB-905 = DIANCHI905
Characteristics strain: FACHB-905 = DIANCHI905
cell type: prokaryotic cell
genotype: WT
treatment: nitrate-N+PS-NH2
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description nitrate-N+PS-NH2
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
 
Submission date Sep 30, 2022
Last update date Sep 01, 2023
Contact name Mei-Yan Liu
E-mail(s) [email protected]
Phone 15238377797
Organization name Shandong university
Street address Aoshanwei Street
City Qingdao
State/province Shandong
ZIP/Postal code 266000
Country China
 
Platform ID GPL32703
Series (1)
GSE214536 Differentially forms of nitrogen regulates the response of Microcystis aeruginosa to nanoplastics under environmentally relevant nitrogen concentration
Relations
BioSample SAMN31109215
SRA SRX17764302

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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