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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 10, 2023 |
Title |
Control, day3, rep1 |
Sample type |
SRA |
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Source name |
C_d3_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: 3
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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 |
SAMN34059727 |
SRA |
SRX19856939 |
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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