|
| Status |
Public on May 30, 2020 |
| Title |
EXOSC3-NPC-3-L002 |
| Sample type |
SRA |
| |
|
| Source name |
Induced Neuronal Progenitor Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast derived iNPCs
genotype: EXOSC3-/-
replicate: 3
sequence lane: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using mirVana miRNA isolation kit (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequence reads were trimmed to 50bp with FastX-toolkit v.0.0.14.
Reads were aligned to complete reference genomes, using the STAR aligner v.2.5.3a.
Transcript counts were obtained with HTSeq v.0.9.1.
Differential expression analysis was performed with DESeq2 v.1.12.4.
Genome_build: hg38 (iNPCs) or danRer11 (zebrafish embryos)
Supplementary_files_format_and_content: text file with per gene read counts generated by HTSeq
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
May 30, 2020 |
| Contact name |
Helen R Griffin |
| E-mail(s) |
helen.griffin@ncl.ac.uk
|
| Phone |
07531816860
|
| Organization name |
Newcastle University
|
| Street address |
William Leech Building, Floor 3, Medical School
|
| City |
Newcatle Upon Tyne |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE151452 |
RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels |
|
| Relations |
| BioSample |
SAMN15054930 |
| SRA |
SRX8424412 |
