|
| Status |
Public on Feb 08, 2021 |
| Title |
SCI3M_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spinal cord
age: 3 mpi (month post-injury)
treatment: Thoracic (T9) moderate contusion injury for 3 months
|
| Treatment protocol |
The mice were conducted with moderate contusive injury with Infinite Horizons impactor (Precision Systems and Instrumentation) at T9 level of the exposed spinal cord (60 kdyn) and mentained for 7 days, 1 month or 3 months
|
| Growth protocol |
Epicenter spinal cord tissue was harvested from SCI mice at 1 month or 3 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation using TRIzol according to detailed manufacturer’s instructions.
Libraries were constructed with the NEBNext Ultra Directional RNA library Prep Kit for Illumina (E7420, New England Biolabs) by following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The quality of all sequenced samples was analyzed using FastQC.
Reads were mapped to the Mm10. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
The gene read counts of samples were normalized and compared to control samples using DESeq2
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Feb 08, 2021 |
| Contact name |
Haichao Wei |
| E-mail(s) |
haichaowei1985@gmail.com
|
| Phone |
3462479690
|
| Organization name |
UTHealth
|
| Street address |
1825 Pressler St., SRB 637.C
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE153720 |
Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis [RNA-Seq] |
| GSE153721 |
Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis |
|
| Relations |
| BioSample |
SAMN15428452 |
| SRA |
SRX8657632 |
