|
| Status |
Public on Jun 02, 2023 |
| Title |
Rat P0 DRG neuron cells_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured P0 DRG neuron cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
type: cDNA
|
| Treatment protocol |
Untreated
|
| Growth protocol |
DRGs were dissociated from rats at P0, followed by digestion with a mixture enzyme of Collagenase I, Trypsin and DNaseI. After centrifugation with 15% Percoll to remove non-neuronal cells, the DRG neurons were obtained and cultured in 35 mm dish (Corning) with the neurobasal medium containing 2% B27 supplement, 2 mM L-Glutamine (Invitrogen) , 100 ng/ml NGF (Invitrogen), 10 mM 5-fluoro-2’-deoxyuridine (Sigma).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from cultured DRG neurons was extracted with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. DRG neurons were cultured 48h in 35 mm dish before rinsed twice with ice-cold PBS, 0.5 mL Trizol was added to the dish for total RNA extraction.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB)
Poly(A)+ RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Rat P0 DRG neuron cells replicate3
|
| Data processing |
Check quality of RNA-seq reads using fastqc (version 0.11.8) with default parameters.
Reads were aligned to rat genome assembly (RGSC Rno5_5.0/rn5) using HISAT2 (Kim et al., 2015) (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10) with annotations from Ensembl (release 79) and RefSeq (updated at 2018/08/27).
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: rn5
Supplementary_files_format_and_content: bigWig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)
|
| |
|
| Submission date |
Jun 02, 2020 |
| Last update date |
Jun 02, 2023 |
| Contact name |
Bin Wang |
| E-mail(s) |
wangbin@sibcb.ac.cn
|
| Phone |
+862154921360
|
| Organization name |
Institute of Brain Science and Brain-Inspired Intelligence, Zhangjiang Laboratory
|
| Street address |
Building No. 12, 100 Haike Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201210 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE151615 |
Axon-enriched lincRNA ALAE is required for axon elongation via regulating local mRNA translation |
|
| Relations |
| BioSample |
SAMN15081167 |
| SRA |
SRX8453064 |
