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| Status |
Public on Apr 07, 2015 |
| Title |
Female1_23a_non-obese_ngt_0h |
| Sample type |
SRA |
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| Source name |
vastus lateralis muscle_female
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| Organism |
Homo sapiens |
| Characteristics |
sample id: P352_125
cell id: 23a
disease: ngt
weight: non-obese
gender: female
time after insulin, h: 0
age: 49
bmi: 23
fasting glucose (0h), mmol/l: 4.9
glucose (2h), mmol/l: 5.5
insulin (0h), pmol/l: 25
insulin (2h), pmol/l: 295
homa-ir: 0.46882325363338
cholesterol (total), mmol/l: 4.3
cholesterol (hdl), mmol/l: 1.5
cholesterol (ldl), mmol/l: 2.3
triglycerides, mmol/l: 0.8
free fatty acids (0h), mmol/l: 0.28
free fatty acids (2h), mmol/l: 0.05
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| Growth protocol |
Muscle precursor cells (satellite cells) were isolated from human skeletal muscle biopsies obtained from the vastus lateralis muscle using a biopsy needle with suction (Bergström, 1975) as described in detail previously (Broholm et al., 2012). Isolated satellite cells were cultured in growth media 1 (HAM/F10 supplied with 20% Fetal Bovine Serum and 1% penicillin/streptomycin) and plated in 6-well plates. Upon 70-80% confluence, the media was changed to differentiation media 1 (DMEM 4.5 g/L glucose supplied with 10% FBS and 1% penicillin/streptomycin) for two-three days, until the myoblasts were completely confluent and had lined up. Hereafter, media was changed to differentiation media 2 (DMEM 4.5 g/L glucose supplied with 2% horse serum and 1% penicillin/streptomycin) thereby initiating fusion into myotubes. Cultures were fully differentiated by day 5 as determined by visual confirmation of myotube formation (>3 nuclei per myotube in ~70% of the cells). Two hours before harvesting of RNA the media was changed to DMEM 1.0 g/L glucose without any supplements.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalling, demultiplexing and conversion using CASAVA v1.8.2.
The reads were trimmed from adapter sequences and aligned to the human genome (Ensembl GRCh37.73, DNA primary assembly) using STAR 2.3.1u and the Homo_sapiens.GRCh37.73.gtf-file. The following additional flags were used: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outStd SAM --outFilterType BySJout
Samtools 0.1.18 was used for indexing and sorting
FPKM-values for each sample were calculated using Cufflinks 2.1.1
Gene counts were calculated using HTSeq-count 0.5.4p3
Genome_build: Ensembl GRCh37.73
Supplementary_files_format_and_content: The count files contain the gene counts for each sample, as output by HTSeq-count. The FPKM-values of all samples are collected into the single file FPKM-values.xlsx.
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| Submission date |
Dec 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Leif Väremo |
| Organization name |
Chalmers University of Technology
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| Department |
Biology and Biological Engineering
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| Street address |
Kemivägen 10
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| City |
Gothenburg |
| ZIP/Postal code |
41296 |
| Country |
Sweden |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE63887 |
RNA-sequencing of healthy human skeletal myocytes |
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| Relations |
| BioSample |
SAMN03253146 |
| SRA |
SRX796618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1559442_P352_125.count.txt.gz |
214.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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