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| Status |
Public on Jun 01, 2019 |
| Title |
C12_fibroblast |
| Sample type |
SRA |
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| Source name |
fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Control
treatment: Fibroblasts were kept 3 days in culture in DMEM, 10 % FBS, 1 % penicillin-streptomycin
cell type: fibroblast
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were prepared using Illumina truseq library kit.
150 cycles paired end RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina bcl2fastq was used for basecalling.
RSEM (1.30) was used to generate expression estimates after alignment to the human transcriptome (Ensembl v.75)
Abundance estiamtes were combined using tximport and normalized using edgeR/limma
Genome_build: GrCH37
Supplementary_files_format_and_content: TSV of normalized counts per gene per patient
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| Submission date |
Jan 17, 2019 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Petter Storm |
| E-mail(s) |
[email protected]
|
| Phone |
+46-40 39 12 27
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| Organization name |
Lund University
|
| Department |
Developmental and Regenerative Neurobiology
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| Street address |
Sölvegatan 19, BMC A11
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| City |
Lund |
| ZIP/Postal code |
22184 |
| Country |
Sweden |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE125239 |
Autophagy impairments in directly reprogrammed neurons in patients with idiopathic Parkinson’s disease |
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| Relations |
| BioSample |
SAMN10762856 |
| SRA |
SRX5257700 |
| 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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