|
| Status |
Public on Apr 05, 2022 |
| Title |
2-CCI12h |
| Sample type |
SRA |
| |
|
| Source name |
spinal cord
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: spinal cord
age: 8 weeks
disease state: chronic constriction injury (CCI)
timepoint: 12h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and then quality controled by agarose gel electrophoresis. After detecting the concentratin, qualified total RNA was enriched with oligo (DT) magnetic beads .If the RNA was degraded or prokaryotic, it was directly treated with rRNA Removal Kit.
RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Library Prep Kit（Illumina）
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Solexa pipeline version 1.8 (off line base caller software, version 1.8) software was used for image processing and base recognition.
Fastqc software was used to evaluate the quality of sequencing, and then the reads of splices were removed with cutadapt after quality filtering by Solexa CHASTITY.
The rat reference genome (UCSC rn6) was compared by Hisat2 software (v2.0.4).
The transcription abundance was estimated by using StringTie software (v1.2.3) referring to the annotation information of official database, and then the Fragments Per Kilobase of exon model per Million mapped reads (FPKM) calculation of gene level was carried out by Balldown software.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 28, 2021 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Changsheng Huang |
| E-mail(s) |
docthuang2005@hotmail.com
|
| Organization name |
Xiangya Hospital, Central South University
|
| Department |
Department of Anesthesiology
|
| Street address |
87 Xiangya Road
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410008 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE175760 |
A Transcriptomic Analysis of Neuropathic Pain in the Spinal Cord after Nerve Injury |
|
| Relations |
| BioSample |
SAMN19405802 |
| SRA |
SRX11017045 |
