|
| Status |
Public on Aug 21, 2018 |
| Title |
Nmd_-_-_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary mouse motoneuron culture
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
tissue: Primary mouse motoneuron culture
genotype: Nmd-/-
|
| Growth protocol |
Motoneurons were obtained and cultured as described in Wiese et al. (Nat Protoc 5: 31-8)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel)
mRNA-Seq Library Prep Kit V2 (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Gene expression data from Nmd-/- motoneurons
|
| Data processing |
Quality Assessment (FASTQC version 0.10.1)
Adapter trimming inlcuding removal of 9 bp from the 5' end of read 1 (TrimGalore version 0.4.0 with Cutadapt version 1.8)
Alignment (Star version 2.5.0a)
Sam-file conversion (Samtools version 1.3)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: csv-files with FPKM-values
|
| |
|
| Submission date |
Feb 28, 2018 |
| Last update date |
Apr 12, 2023 |
| Contact name |
Silke Appenzeller |
| E-mail(s) |
[email protected]
|
| Organization name |
University Wuerzburg
|
| Street address |
Schweinfurter Str. 28
|
| City |
Würzburg |
| ZIP/Postal code |
97076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE111224 |
Impaired local translation of β-actin mRNA in Ighmbp2-deficient motoneurons: implications for spinal muscular atrophy with respiratory distress (SMARD1) |
|
| Relations |
| BioSample |
SAMN08619824 |
| SRA |
SRX3749093 |
