RNA-Seq of mus musculus - SRA

SRX16221945: RNA-Seq of mus musculus
1 BGISEQ (BGISEQ-500) run: 23.8M spots, 713.6M bases, 751.5Mb downloads

Design: Briefly, to extract the total RNA, a total of 200 L serum sample were added with 1 mL QIAzol lysis reagent, vortexed well, and incu bated at room temperature for 5 min. Then, a total of 200 L chloroform/isoamyl alcohol (24:1; v/v) were added to the sample, vortexed vigorously for 15 s, and incubated at room temperature for 23 min. The samples were centrifuged at 12,000 g and 4 C for 8 min to collect the supernatant (5427R, Eppendorf Co., Ltd., Beijing, China), added with absolute ethanol twice the volume of the supernatant, and the mixture was column purified and washed once with 700 L RWT buffer and washed twice with 500 L RPE buffer (QIAgen, Beijing, China). The samples were centrifuged at 12,000 g and room temperature for 2 min with the purification column removed and replaced with a new collection tube, added with 20 L RNA free water, and incubated at room temperature for 1 min. Finally, the mixture was centrifuged at 12,000 g and room temperature for 2 min to elute RNA. The concentrations of eluted RNAs were determined with an Agilent 2100 Bioanalyzer (Agilent Technologies Co., Ltd., Beijing, China). The libraries for high-throughput miRNA sequencing were constructed based on the segments of 1830 nt separated by PAGE gels (430 ssRNA Ladder Marker, TAKARA). The connections of both 3 and 5 adaptor systems and the RT-PCR analysis were performed by following the procedures provided by the manufacturers. The double stranded PCR products were denatured and then circularized by the splint oligo sequence to generate the single strand circle DNAs (ssCir DNAs), which were formatted as the final library. The final library was validated by the Agilent 2100 Bioanalyzer and amplified with phi29 to generate the DNA nanoball (DNB) with more than 300 copies of one molecule. The DNBs were loaded into the patterned nanoar ray to generate the single end 50 bp reads based on the combinatorial Probe-Anchor Synthesis (cPAS). The raw data were processed to generate the clean tags based on the manufacturers instructions. The clean tags were mapped onto the genome of Mus musculus with the reference version of GCF_000001635.26_GRCm38.p6 of the BioProject 320 PRJNA20689 at the National Center for Biotechnology Information database (https://www.ncbi.nlm.nih.gov/assembly/; accessed on 21 April 2019) and further annotated based on miRbase database (http://www.mirbase.org/; accessed on 21 April 2019) and Rfam database (https://rfam.xfam.org/; accessed on 21 April 2019) with Bowtie2 .

Submitted by: College of Biological and Food Engineering, Jilin Engineering Normal University

Study: Molecular and Biochemical Investigations of the Anti-Fatigue Effects 2 of Tea Polyphenols and Fruit Extracts of Lycium ruthenicum Murr. on 3 Mice with Exercise-Induced Fatigue

PRJNA858659 • SRP386386 • All experiments • All runs

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The molecular mechanisms underlying the exercise-induced fatigue (EIF) remain unclear.We investigated the therapeutic effects of both tea polyphenols (TP) and fruit extracts of Lycium ruthenicum (LR) on mouse model of EIF. Our results revealed that both TP and LR showed evident anti-inflammatory effect and reduced oxidative stress, i.e., significantly altered contents of fatigue-related biochemical indices, including lactate dehydrogenase, superoxide dismutase, interleukin-2, interleukin-6, et al, in mice with EIF. A total of 23 microRNAs (21 up-regulated and 2 down-regulated) identified for the first time by the high-throughput RNA sequencing were involved in the molecular response to EIF in mice treated with TP and LR. The regulatory functions of these microRNAs in the pathogenesis of EIF in mice were further explored based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Our results revealed the therapeutic effects of TP and LR and identified the microRNAs involved in the molecular mechanisms regulating the EIF in mice, providing strong experimental evidence to support further agricultural development of LR and investigations and applications of TP and LR in the treatment of EIF in humans, including the professional athletes.

Sample:

SAMN29723139 • SRS13862993 • All experiments • All runs

Organism: Mus musculus

Library:

Name: 5

Instrument: BGISEQ-500

Strategy: miRNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Runs: 1 run, 23.8M spots, 713.6M bases, 751.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR20187073	23,803,216	713.6M	751.5Mb	2023-06-15

ID:: 22926835

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