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| Status |
Public on Jun 30, 2020 |
| Title |
47-MB-A |
| Sample type |
SRA |
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| Source name |
Human primary myoblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell type: myoblast
disease status: Control
gender: F
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| Growth protocol |
LCLs were obtained from NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research (CIMR) repository, NJ 08103, USA. Lymphoblastoid FSHD cell lines GSM16283, GSM16414, GSM16278 and respective matched control lines GSM16281, GSM16320,GSM16412 were from two directly related families from Southern Utah, USA. LCLs were cultured in suspension in RPMI-1640 medium, supplemented with L-glutamine, sodium bicarbonate (Sigma), 10% foetal bovine serum(FBS) (Sigma) and gentamycin (Gibco). Cell pellets were collected from three independent flasks for each cell line
Cell pellets corresponding to FSHD primary myoblast cell lines FSHD3 (FSHD1, 7RU, female), FSHD6 (FSHD1, 8RU, female) and FSHD9 (FSHD1, 7RU, male) alongside age and sex matched controls, in proliferation and after three days of differentiation into multinucleated myotubes, in singlet, were kind gifts from Dr Dalila Laoudj-Chenivesse (University of Montpellier, Montpellier, France).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using miRNeasy kit (Qiagen) including a DNAse digestion step. RNA was analysed by LabChip Bioanalyzer, Qubit fluorometric quantification and Nanodrop quantification of concentration and stability
RNA-seq libraries were prepared using the sureselect stranded RNAseq protocol (Illumina), which allows polyA selection but was modified to work with ribodepletion (Agilent). Libraries were sequenced on an Illumina HiSeq2500
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CTRL9-MB
Primary_Myoblasts_Myotubes_gene_counts.txt
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| Data processing |
Raw reads were trimmed using trim-galore, utilising cutadapt14 (v0.4.0) to remove the Illumina Sequencing Adapter (AGATCGGAAGAGC) at the 3' end. Additionally, 12 bases were also trimmed from the 5' end, in both myoblast and LCL samples and 5 bases from the 3' end in the LCL samples, since they showed a biased distribution. Reads were mapped to the human transcriptome using the human genome sequence GRCh38 and v82 gene annotations downloaded from Ensembl. Mapping was performed using tophat 15 (v2.1.0) and bowtie 16 (v1.1.0), enabling the fr-firststrand option of tophat to restrict mapping to the sense strand of the transcript. Reads were assigned to genes using the featureCounts program 17 (v1.5.0), counting fragments and ignoring multi-mapping reads, and restricted to the sense strand. The resulting matrix of read counts was analysed using R. Data describing the myoblast and LCLs were processed in separate batches and therefore analysedas separate datasets. Both datasets were normalised using the DESeq2 package (71)in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count files
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| Submission date |
Jun 29, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Christopher Raja Socrates Banerji |
| E-mail(s) |
cb4115@ic.ac.uk
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| Organization name |
King's College London
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| Department |
Randall Division of Cell and Molecular Biophysics
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| Lab |
Zammit Lab
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| Street address |
New Hunts House
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| City |
London |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE153523 |
DUX4-expressing immortalised FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation |
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| Relations |
| BioSample |
SAMN15401061 |
| SRA |
SRX8635230 |
| 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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