|
| Status |
Public on Aug 31, 2024 |
| Title |
Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal root ganglion(DRG) neuron
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Dorsal root ganglion(DRG) neuron
strain: B6
genotype: RPL22HA+/+;Advillin-Cre+/-
developmental stage: adult
treatment: Preconditioning(Sciatic nerve injury)
in vitro_viral_gene_delivery: AAV-control
ip antibody: Anti-HA tag(abcam, #ab9110)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Ribotag-RNA sequencing, lysate from the freshly collected cultured DRG neurons were immunoprecipitated with an anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using Rneasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (Nanopore, cDNA-PCR barcoding kit(SQK-PCB111.24))
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
control.tsv
|
| Data processing |
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts
|
| |
|
| Submission date |
Aug 12, 2024 |
| Last update date |
Aug 31, 2024 |
| Contact name |
Yongcheol Cho |
| E-mail(s) |
[email protected]
|
| Phone |
82-53-785-6190
|
| Organization name |
DGIST
|
| Department |
Department of Brain Sciences
|
| Lab |
Axon Regeneration and Degeneration
|
| Street address |
333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun
|
| City |
Dalseonggun, Daegu |
| State/province |
Daegu |
| ZIP/Postal code |
42988 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24973 |
| Series (1) |
| GSE274619 |
Ribotag-RNA sequencing data using Csde1-KD dorsal root ganglion(DRG) neurons |
|
| Relations |
| BioSample |
SAMN43150807 |
| SRA |
SRX25677291 |
