|
| Status |
Public on Feb 13, 2023 |
| Title |
SN4741_RNAseq_39_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SN4741
|
| Organism |
Mus musculus |
| Characteristics |
cell line: SN4741
cell type: Neural precursor cells
genotype: WT
treatment: 39°C Incubation
|
| Treatment protocol |
To induce differentiation, 24 hours after the cells were passaged, media was replaced by DMEM supplemented with 1% penicillin–streptomycin and 0.5% FBS at 39°C. Cells were allowed to grow and differentiate in these conditions for 48 hours before harvesting for experimentation.
|
| Growth protocol |
SN4741 cells were maintained in high glucose Dulbecco's Modified Eagle Medium, supplemented with 1% penicillin–streptomycin and 10% fetal bovine serum in a humidified 5% CO2 incubator at 37°C. Cells at 80% confluence were passaged by trypsinization approximately every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were run through QIAshredder (Qiagen) and total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations, except that RNA was eluted twice in 50μL of water. Total RNA integrity was determined with the RNA Pico Kit (Agilent) on the Agilent 2100 Bioanalyzer.
Library preparation was done using NEBNext Ultra II directional library prep kit with poly-A selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files were aligned to the mouse reference genome (mm10) with HISAT2 (v2.0.5) and sample reads from different lanes were merged using samtools (v.1.10) function “merge.”.
Aligned reads from individual samples were quantified against the mm10 reference transcriptome with the subread (v1.6.1) function “featureCounts”, using -t exon and -g gene_id.
Assembly: mm10
|
| |
|
| Submission date |
Feb 10, 2023 |
| Last update date |
Feb 13, 2023 |
| Contact name |
Andrew S. McCallion |
| E-mail(s) |
andy@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Genetic Medicine
|
| Lab |
McCallion
|
| Street address |
733 North Broadway
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE225071 |
Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons [Bulk RNA-seq] |
| GSE225084 |
Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons |
|
| Relations |
| BioSample |
SAMN33244631 |
| SRA |
SRX19333742 |
