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Sample GSM4990954

Query DataSets for GSM4990954

Status

Public on Dec 29, 2020

Title

FM-C-01

Sample type

SRA

Source name

plasma

Organism

Homo sapiens

Characteristics

treatment: symptomatic and supportive treatment

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.

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.

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina NextSeq 500

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

Submission date

Dec 28, 2020

Last update date

Dec 30, 2020

Contact name

Jing Wang

E-mail(s)

legend@fudan.edu.cn

Phone

+86 15168863836

Organization name

Shandong Provincial Hospital