|
| Status |
Public on Jan 16, 2024 |
| Title |
cerebellum, Ctrl, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
cerebellum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cerebellum
genotype: WT
time: Day 20
|
| Growth protocol |
20 day old mice were euthanized and cortex, hippocampus and cerebellum were dissected on ice, fast frozen, and stored in -80˚C until RNA extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
On the day of RNA extraction, 50-100mg tissue from each sample was lysed in 1ml TRIzol (Invitrogen, #15596026) according to the manufacturer’s recommendations.
mRNA-seq libraries were generated at Novogene and sequenced on an Illumina NovaSeq 6000 platform with 2x150 PE configuration at an average of 15 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter and poor quality sequences were trimmed and cleaned mRNA reads mapped to the Mus musculus GRCm38 reference genome using STAR (v2.7.3a).
Reads were counted using FeatureCounts from the subread package (v2.0.1) with parameters: -p -C -O.
Differential gene expression analysis was performed with DEseq2 (V1.38.3) excluding genes with less than five reads, and all genes from chromosome X and Y. Differential expression was performed using a linear model and as factor the genotypes.
Assembly: GRCm38
Supplementary files format and content: Coverage files in BigWig format
|
| |
|
| Submission date |
Jan 11, 2024 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Naiara Akizu |
| E-mail(s) |
aquizun@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Pathology And Lab Medicine
|
| Lab |
Akizu Lab
|
| Street address |
3501 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE253045 |
IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency |
|
| Relations |
| BioSample |
SAMN39406598 |
| SRA |
SRX23165850 |
