|
| Status |
Public on Dec 07, 2021 |
| Title |
Human_skeletal_muscle_cells_TGFB1_rep3 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Human skeletal muscle cells treated with TGF-β1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Skeletal muscle cells
treatment: TGF-beta1
|
| Treatment protocol |
As described in the paper. Briefly, stimulations with TGF-β1 were performed two days before initiation for 48 h, or during myotube differentiation for 96 h or 48 h as indicated. Human TGF-β1 (R&D Systems) was dissolved in 4 mM HCl 0.2% BSA while SB431542 (Milteny Biotech) was dissolved in DMSO.
|
| Growth protocol |
As described in the paper. Briefly, human satellite cells were obtained by percutaneous needle biopsies performed on vastus lateralis muscle. Cells were released by collagenase digestion and seeded on 15-cm dishes coated with GelTrex (thin layer protocol, 1:300, Life Technologies). After two rounds of proliferation in cloning medium (39% α-MEM, 39% Ham’s F-12, 20% FBS, 1% chicken extract, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.5 μg/ ml amphotericin B), CD56-positive myoblasts were enriched using MACS microbeads and LS-columns (Milteny Biotech) according to the manufacturer’s protocol, with 30 min incubation and stored in the gaseous phase of liquid nitrogen. For experiments, cells were seeded at 1000 cells/cm² in cloning medium on 6well plates. Myotube differentiation was initiated by either 2% FBS or FBS-free fusion medium (α-MEM, 100 U/ml penicillin, 50 μM palmitate, 50 μM oleate, 100 μM carnitine, 100 μg/ml streptomycin, 0.5 μg/ml amphotericin B) and continued for 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin miRNA kit (Macherey-Nagel).
Ovation RNA-Seq System V2 for cDNA synthesis, amplification and purification. Libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TGFB1_3
|
| Data processing |
Fastq files were generated with CASAVA BCL2FASTQ Conversion Software.
TrimGalore (v0.6.6, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Read mapping with STAR v2.7.6a.
Normalization was done using DESeq2 v1.32.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with normalized counts for each sample.
|
| |
|
| Submission date |
Nov 04, 2021 |
| Last update date |
Dec 07, 2021 |
| Contact name |
Johannes Beckers |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Zentrum Muenchen
|
| Department |
Institute of Experimental Genetics
|
| Street address |
Ingolstaedter Landstr. 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE188234 |
TGF-β-induced miR143/145 influences differentiation, insulin signaling and exercise response in human skeletal muscle [RNA-seq] |
| GSE188236 |
TGF-β Induction of miR-143/145 Is Associated to Exercise Response by Influencing Differentiation and Insulin Signaling Molecules in Human Skeletal Muscle |
|
| Relations |
| BioSample |
SAMN22895853 |
| SRA |
SRX12975687 |
