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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2023 |
| Title |
Control, day0, rep1 |
| Sample type |
SRA |
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| Source name |
C_d0_1
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: m. soleus
cell line: fibro-adipogenic progenitor cells
cell type: primary cells
treatment: Control
day of_hs: 0
day of_differentiation: 0
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| Treatment protocol |
Cells were isoleted and cultured to subconfluent state.
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| Growth protocol |
Fibro-adipogenic progenitor cells (FAPs) were cultured in DMEM supplemented with 1% penicillin-streptomycin, 1% L-glutamine, 10% FBS (HyClone, USA) on cell culture dishes. Adipogenic differentiation of FAPs was stimulated by replacing the culture media with adipocyte induction medium composed of culture medium supplemented with 1 μM insulin, 1 μM dexamethasone, and 0,5 μM 3-isobutyl-1-methylxanthine.
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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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| 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 12 Samples
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| Submission date |
Apr 03, 2023 |
| Last update date |
Apr 10, 2023 |
| 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) |
| GSE228869 |
Functional unloading leads to metabolic and functional disorders in FAPs in vitro |
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| Relations |
| BioSample |
SAMN34059729 |
| SRA |
SRX19856937 |
| 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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