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| Status |
Public on Dec 07, 2021 |
| Title |
Human_skeletal_muscle_cells_TGFB1_SB431542_rep3 [small RNA-seq] |
| Sample type |
SRA |
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| Source name |
Human skeletal muscle cells treated with TGF-β1 and the SB431542 inhibitor
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Skeletal muscle cells
treatment: TGF-beta1 + SB431542 inhibitor
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| 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.
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin miRNA kit (Macherey-Nagel).
Small RNA library preparation using NEBNext Small RNA Library Prep Set for Illumina (New England BioLabs).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
TGFB1_SB_3
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| Data processing |
Raw data was collected by the Illumina HiSeq Control Software (version 2.2.58). Illumina Real-Time Analysis tool (version 1.18.64) was used for image analysis and base calling. The single-end sequence reads with 50 base pair read length were demultiplexed and FASTQ files were generated with CASAVA BCL2FASTQ Conversion Software (version 1.8.3).
Trim Galore (v0.0.4, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim reads of all analyzed data sets in two steps. In the first step, all adapters were removed and only reads shorter than the maximum sequencing length were kept. In the second step, reads were trimmed for a minimum quality threshold of 20.
We used STAR v2.5.2a to map the trimmed reads to the primary assembly of the human reference genome GRCh38. STAR was configured to match at least 16 nucleotides with a maximum of 5% mismatches over the mapped length having the splicing function switched off.
Normalization was done using DESeq2 v1.22.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with normalized counts for each sample.
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| Submission date |
Nov 04, 2021 |
| Last update date |
Dec 07, 2021 |
| Contact name |
Johannes Beckers |
| E-mail(s) |
[email protected]
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| Organization name |
Helmholtz Zentrum Muenchen
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| Department |
Institute of Experimental Genetics
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| Street address |
Ingolstaedter Landstr. 1
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| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE188235 |
TGF-β-induced miR143/145 influences differentiation, insulin signaling and exercise response in human skeletal muscle [small 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 |
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| Relations |
| BioSample |
SAMN22895874 |
| SRA |
SRX12975787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5673220_TGFB1_SB_3.txt.gz |
6.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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