|
| Status |
Public on May 12, 2021 |
| Title |
oxaliplatin rep4 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal root ganglion
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Dorsal root ganglion
treatment: Oxaliplatin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rats DRGs were flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library kit was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
mRNA
|
| Data processing |
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Genome_build: NA
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include reads count values for each Sample.
|
| |
|
| Submission date |
Oct 30, 2020 |
| Last update date |
May 14, 2021 |
| Contact name |
SHAO MIN YANG |
| E-mail(s) |
shaominyang@stu2020.jnu.edu.cn
|
| Organization name |
Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
|
| Department |
Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
|
| Street address |
Nanshan
|
| City |
Shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL24782 |
| Series (1) |
| GSE160543 |
Comparison of the transcriptional changes in dorsal root ganglion between paclitaxel and oxaliplatin induced peripheral neuropathic pain in rats |
|
| Relations |
| BioSample |
SAMN16615420 |
| SRA |
SRX9409857 |
