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Status |
Public on Apr 25, 2022 |
Title |
Control, rep2 |
Sample type |
SRA |
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Source name |
m. soleus
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Organism |
Rattus norvegicus |
Characteristics |
tissue: m. soleus cell line: skeletal muscle progenitor cells cell type: primary cells treatment: Control day: 0
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Treatment protocol |
Cells were isoleted and cultured to subconfluent state.
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Growth protocol |
Skeletal muscle progenitor cells were cultured in DMEM supplemented with 1% penicillin-streptomycin, 1% L-glutamine, 1% chicken fetal serum (USBiological, USA), 20% FBS (HyClone, USA), 10 % horse-serum (Gibco, USA)) on cell culture dishes covered with Geltrex (1:100 in cold DMEM, 1,5 hours at 37℃, Invitrogen, USA).
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia) Libraries were constructed using TruSeq Stranded mRNA library prep kit
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
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Description |
С_2
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Data processing |
Read quality was checked for each sample using FastQC v0.11.9. Sequenced reads were mapped to the mouse genome using mapper STAR v2.7 with rat reference genome Rnor_6.0 (Ensembl release 104) and annotation Rnor_6.0.104.chr.gtf Aligned reads were count with featureCounts program v1.6.4. Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools. Assembly: Genome Rnor_6.0 (Ensembl release 104) Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 10 Samples
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Submission date |
Apr 22, 2022 |
Last update date |
Apr 25, 2022 |
Contact name |
Margarita Sorokina |
E-mail(s) |
komarovamy96@yandex.ru, sorokinamy96@yandex.ru
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Organization name |
Almazov National Medical Research Centre
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Street address |
Akkuratova 2
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City |
Saint-Petersburg |
ZIP/Postal code |
197341, 123007 |
Country |
Russia |
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Platform ID |
GPL32190 |
Series (1) |
GSE201281 |
Skeletal muscle unloading affects muscle progenitor cells functional activity |
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Relations |
BioSample |
SAMN27737659 |
SRA |
SRX14964094 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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