|
| Status |
Public on Feb 26, 2019 |
| Title |
Patient 2 |
| Sample type |
SRA |
| |
|
| Source name |
patient_cultured human fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: patient with a mutation in the ELOVL1 gene
gender: male
genotype/variation: ELOVL1 p.S165F
tissue: skin biopsy from the forearm
cell type: fibroblasts
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Culture of fibroblasts in DMEM supplemented with 15% FBS and 1% penicillin/streptomycin at 37°C in 5% carbondioxide until semi-confluency and yielded by trypsinization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with the TRIzol protocol
BGISEQ-500 RNA-Seq library (depletion of tRNAs and of rRNAs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Patient_2
Patient_2_HK500HUMxdhRAABRBAPEI-3-4-3_1
|
| Data processing |
Quality check and trimming of adapter sequences were done with FastQC
The alignment to the human reference sequence (hg19) was done with STAR 2.4.0.1
Transcriptiome analysis was performed with the CUFFLINKS 2.2.1 pipeline
Calculation of FPKM values was done with CUFFQUANT
Calculation of differential gene expression CUFFDIFF
Genome_build: GRCh37.p11 (hg19)
Supplementary_files_format_and_content: CUFFLINKS output files
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Feb 26, 2019 |
| Contact name |
Markus Schuelke |
| E-mail(s) |
markus.schuelke@charite.de
|
| Phone |
++49 30 4505 66112
|
| Organization name |
Charite
|
| Department |
Neuropediatrics
|
| Lab |
Schuelke lab
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE116986 |
De novo mutation in ELOVL1 causes ichthyosis, acanthosis nigricans, and hypomyelination with lower extremity spastic paraplegia, high frequency deafness, and tunnel vision. |
|
| Relations |
| BioSample |
SAMN09649872 |
| SRA |
SRX4383917 |
