|
| Status |
Public on Sep 05, 2024 |
| Title |
SOD1-A4V VEH DIFF1 |
| Sample type |
SRA |
| |
|
| Source name |
SOD1-A4V
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SOD1-A4V
cell type: iPSC-derived Astrocytes
genotype: ALS
treatment: VEH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAeasy mini kit (Qiagen). 1.6ug of total RNA for each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library prep kit using manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ElementBio AVITI
|
| Data processing |
Sequence reads were trimmed using FastX 0.0.14
Trimmed sequence reads were mapped to reference genome Homo_sapiens.Ensembl.GRCh38.88 using STAR 2.5.2b (parameters: --outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate)
Reads in the alignments that overlap with gene features were counted using featureCounts 1.5.3 (parameters: -Q 0 -s 2 -t exon -g gene id)
Normalization of counts for each sample was performed using EDASeq.
Assembly: Homo_sapiens.Ensembl.GRCh38.88
Supplementary files format and content: tab-delimited .txt file containing raw counts for each sample
Supplementary files format and content: tab-delimited .txt file containing FPKM values for each sample
|
| |
|
| Submission date |
Mar 05, 2024 |
| Last update date |
Sep 05, 2024 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE260913 |
Targeting EGLN2/PHD1 protects motor neurons and normalizes the astrocytic interferon response. |
|
| Relations |
| BioSample |
SAMN40268882 |
| SRA |
SRX23842086 |
