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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2021 |
| Title |
VSMCs, si-circ-2 |
| Sample type |
SRA |
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| Source name |
mouse vascular smooth muscle cells (VSMCs)
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| Organism |
Mus musculus |
| Characteristics |
passage: 4-10
strain: C57BL/6
cell type: mouse vascular smooth muscle cells (VSMCs)
treatment: circEsyt2 siRNA (si-circ)
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| Growth protocol |
Mouse vascular smooth muscle cells (VSMCs) were transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ) for 48 hours, respectivly.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Sep 01, 2020 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Xue Gong |
| Organization name |
Army Medical University
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| Street address |
Changjiang branch Road
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| City |
Chongqing |
| ZIP/Postal code |
400042 |
| Country |
China |
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| 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) |
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| Relations |
| BioSample |
SAMN15960574 |
| SRA |
SRX9053271 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4760985_C3.FPKM.csv.gz |
323.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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