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Sample GSM6846618

Query DataSets for GSM6846618

Status

Public on Dec 16, 2022

Title

siNC-3 in 293T

Sample type

SRA

Source name

Human HEK293T cells

Organism

Homo sapiens

Characteristics

tissue: HEK293T cells
treatment: transfection of non-specific siRNA for 24 hours

Extracted molecule

total RNA

Extraction protocol

TruSeq Small RNA Library Preparation Kits (Illumina) (for small RNAs); MGIEasy RNA Library Preparation Kits (BGI) (for total RNAs)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MGISEQ-2000RS

Description

total RNA

Data processing

Fo small RNAs, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were mapped to the human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0) by using Bowite 2.2.5, and the cellular miRNA expression level was determined on the basis of the number of reads, which were 100% identical to the annotated miRNA sequences in miRBase version 22 (https://www.mirbase.org/ftp/CURRENT/genomes/dme.gff3). The vsRNA reads that cannot be mapped to the host genome were then mapped to the viral genome allowing 2 nt mismatch. The vsRNA reads were counted and normalized by the number of total vsRNA reads (counts per million of total vsRNA reads) to show the size distribution and abundance of vsRNAs in different size, and 21-23 nt size vsRNA reads mapping to the viral genome were counted to show the distribution across the viral genome. The vsRNA Reads mapped to (+)-strand and (-)-strand of the viral genome were intersected using BedTools (v2.29.2).
For total RNAs, libraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. Then all reads were mapped to the human genome (release hg19) using Hisat2. DEseq2 (v1.34.0) was used to detect differentially expressed genes.
Assembly: Human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0)

Submission date

Dec 16, 2022

Last update date

Dec 16, 2022

Contact name

Yang Qiu

E-mail(s)

yangqiu@wh.iov.cn

Organization name

Wuhan institue of virology, CAS

Street address

No. 44 Xiaohongshan Central District, Wuchang District,