|
| Status |
Public on Feb 26, 2024 |
| Title |
DRGaxon |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Root Ganglion
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Dorsal Root Ganglion
strain: C57BL/6
developmental stage: embryonic day 13.5
|
| Treatment protocol |
Neurons are cultured in microfluidic chamber to separate axons from soma.
|
| Growth protocol |
Dissociated dentate gyrus granule cells were cultured in Neurobasal A-medium with B27 supplement, GlutaMAX-1, and Penicillin-Streptomycin. Dissociated dorsal root ganglion cells were cultured in Neurobasal medium with B27 supplement, GlutaMAX-1, Penicillin-Streptomycin, 5FdU and NGF. Dissociated retinal ganglion cells were cultured in Neurobasal medium with GlutaMAX-1, cAMP, Froskolin, N2 and B27 supplement, Penicillin-Streptomycin and growth factors inclduing NT3, BDNF, EGF, FGF2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
none
|
| Data processing |
The raw data was used fastp to filter low-quality reads.
The filtered reads were mapped to the mouse reference genome (mm10) using STAR v2.7.8a.
The resulting bam files were fed to featureCounts tool to count the number of RNA-seq reads.
The number of RNA-seq reads was further normalized to calculate TPM.
Specific genes were analyzed by comparing the gene expression of different samples.
Assembly: mm10
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Zhuoxuan Yang |
| E-mail(s) |
12032900@mail.sustech.edu.cn
|
| Phone |
17604514873
|
| Organization name |
Southern University of Science and Technology
|
| Street address |
No. 1088 Xueyuan Avenue, Nanshan District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE201547 |
RNA-sequencing to idendify axon RNAs in dentate gyrus granule cells, dorsal root ganglion cells and retinal ganglion cells |
|
| Relations |
| BioSample |
SAMN27779473 |
| SRA |
SRX15000621 |
