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Sample GSM4760982 Query DataSets for GSM4760982
Status Public on Dec 31, 2021
Title VSMCs, scr-1
Sample type SRA
 
Source name mouse vascular smooth muscle cells (VSMCs)
Organism Mus musculus
Characteristics passage: 4-10
strain: C57BL/6
cell type: mouse vascular smooth muscle cells (VSMCs)
treatment: control
Growth protocol Mouse vascular smooth muscle cells (VSMCs) were transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ) for 48 hours, respectivly.
Extracted molecule total RNA
Extraction protocol VSMCs were washed twice in cold PBS and lysed in RNAiso (Takara, Cat# 108-95-2) before sent to BioWavelet (Chongqing, China) for sequencing. The first-strand of cDNA was synthesized using SuperScript III reverse transcriptase (Invitrogen, Cat# 18080-085) followed by the second-strand synthesis using synthesis enzyme mix (Biowavelet, Cat# BWR001) according to guidelines.
RNA libraries were prepared using TruePrep DNA Library Prep Kit for Illumina (Vazyme, Cat# TD503) according to the standard protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Hiseq control software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to the GRCm38/mm10 mouse reference genome using hisat2 and mapped to gene using bowie2.
Gene expression was caculated based on FPKM (Fragments per Kilobase of exon model per Million mapped fragments) using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include FPKM values for each sample
 
Submission date Sep 01, 2020
Last update date Dec 31, 2021
Contact name Xue Gong
Organization name Army Medical University
Street address Changjiang branch Road
City Chongqing
ZIP/Postal code 400042
Country China
 
Platform ID GPL21493
Series (1)
GSE133270 RNA expression profiles of mouse vascular smooth muscle cells (VSMCs) transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ)
Relations
BioSample SAMN15960578
SRA SRX9053268

Supplementary file Size Download File type/resource
GSM4760982_A1.FPKM.csv.gz 314.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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