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| Status |
Public on Aug 22, 2017 |
| Title |
EXOSC3_patient |
| Sample type |
SRA |
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| Source name |
quadiceps muscle of EXOSC3 patient
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| Organism |
Homo sapiens |
| Characteristics |
mutation: EXOSC3 c.395A>C (NM_016042), p.(D132A)
gender: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
fresh muscle biopsy, flash frozen in liquid nitrogen, TRIzol extraction of RNA
BGISEQ-500 RNA-seq, single end 50 bp, unstranded
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
91 Mio FASTQ reads were aligned to the human reference sequence (GRCh37.75) with the STAR 2.4.0.1 aligner.
Resulting BAM files were investigated and normalized with the CUFFLINKS 2.2.1. pipeline (CUFFLINKS>CUFFMERGE>CUFFQUANT>CUFFNORM).
As the quantitative measure for gene abundance we used the FPKM value (fragments per kilobase of transcript per million mapped reads), which is calculated by the CUFFQUANT module of the CUFFLINKS software.
In order to render the highly different absolute FPKM expression levels comparable on the same graph, we provide the z-score for each gene, which is calculated using the mean and the SD of the 6 controls according to z-scorepatient = (mean(FPKM)controls – FPKMpatient)/SD(FPKM)controls.
Genome_build: Homo sapiens GRCh37.75
Supplementary_files_format_and_content: FPKM
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| Submission date |
Jun 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Markus Schuelke |
| E-mail(s) |
markus.schuelke@charite.de
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| Phone |
++49 30 4505 66112
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| Organization name |
Charite
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| Department |
Neuropediatrics
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| Lab |
Schuelke lab
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| Street address |
Augustenburger Platz 1
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE99715 |
Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia |
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| Relations |
| BioSample |
SAMN07197339 |
| SRA |
SRX2885453 |
| 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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