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Status |
Public on Dec 29, 2020 |
Title |
FM-C-03 |
Sample type |
SRA |
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Source name |
plasma
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Organism |
Homo sapiens |
Characteristics |
treatment: symptomatic and supportive treatment
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Treatment protocol |
Total RNAs that were extracted from plasma were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.
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Extracted molecule |
total RNA |
Extraction protocol |
The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Raw data files in FASTQ format were generated from the Illumina sequencer. After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format. Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001 The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA. Genome_build: GtRNAdb, tRFdb Supplementary_files_format_and_content: text file with abundance
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Submission date |
Dec 28, 2020 |
Last update date |
Dec 30, 2020 |
Contact name |
Jing Wang |
E-mail(s) |
legend@fudan.edu.cn
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Phone |
+86 15168863836
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Organization name |
Shandong Provincial Hospital
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Street address |
No. 324, jingwuweiqi road, huaiyin district
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City |
Jinan |
ZIP/Postal code |
250021 |
Country |
China |
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Platform ID |
GPL18573 |
Series (1) |
GSE163944 |
Differential expression profiles of plasma tsRNAs in children with fulminant myocarditis |
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Relations |
BioSample |
SAMN17172172 |
SRA |
SRX9742380 |
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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