|
| Status |
Public on Jan 19, 2023 |
| Title |
RNA-seq primary fibroblast WT2 |
| Sample type |
SRA |
| |
|
| Source name |
primary cutaneous fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
proband: WT2
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Primary patient-derived Fibroblast cells were cultured at 5% CO2 and 37°C in high glucose DMEM (HyClone) supplemented with 10% fetal bovine serum (FBS) (HyClone), 1X penicillin/streptomycin (Thermo Fisher Scientific) and 2 mM L-glutamine (Biological Industries)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from primary dermal fibroblasts was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing according to standard manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the default parameters to the human GRCh38.p12 reference genome. The alignment was performed with the GENCODE annotation v28.
Quantification: Transcript abundance of the annotated genes from GENCODE v2852 using HTSeq v0.11.453 in 'union' mode.
Genome_build: Human (hg38/GRCh38)
Supplementary_files_format_and_content: bigWig files: transcript coverage of uniquely mapped reads.
|
| |
|
| Submission date |
Feb 21, 2022 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Dr. Andreas Mayer |
| Organization name |
Max-Plack-Institute for molecular genetics
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE197118 |
A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele [RNA-seq] |
| GSE197120 |
A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele |
|
| Relations |
| BioSample |
SAMN26137515 |
| SRA |
SRX14241587 |
