|
| Status |
Public on Jul 23, 2024 |
| Title |
Spinal Cord B3 |
| Sample type |
SRA |
| |
|
| Source name |
Spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spinal cord
cell type: T cells
gender: female
age: 24 months
strain: C57BL/6J
treatment: spinal cord injury
|
| Treatment protocol |
Before being assigned to surgery, the body weight of mice was assessed and mice lighter than 19 grams were removed. Mice were anesthetized with a ketamine (100 mg kg-1)–xylazine (10 mg kg-1) mixture. The hair on the back was shaved and cleaned with betadine and alcohol. A 15-mm midline skin incision was performed over the T6-T13 vertebra, and the connective and muscle tissues were bluntly dissected to expose the lamina. A laminectomy was performed using rongeurs at T9 to expose the dorsal spinal cord. The vertebral column was stabilized with angled clamps attached to the T7 and T12 and a calibrated contusion injury of the spinal cord was induced at T9 by an Infinite Horizon Impactor (IH-0400 Impactor Precision Systems and Instrumentation) at a force of 80K dynes. After the injury, the muscles and skin were sutured separately and mice were allowed to recover from anesthesia on heating pads. After recovering from anesthesia, mice were injected intra-subcutaneously with buprenorphine (0.05 mg kg-1) daily for the first three days. Water containing sulfamethoxazole and trimethoprime oral suspension (200 mg/ 40 mg L-1) was supplied. Soft food and nutra-gel diet (S5769-TRAY, Bio-Serv) were supplied daily. Bladders of all mice were manually voided twice a day during the experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See 'overall design' on Series record.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA was isolated from 6 mice.
|
| Data processing |
Demultiplexing with custom Python and perl script.
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Assembly: mm10
Supplementary files format and content: all.gene_counts.csv: Comma-separated text file with raw gene counts for all cells.
|
| |
|
| Submission date |
Oct 23, 2022 |
| Last update date |
Jul 23, 2024 |
| Contact name |
Jonathan Kipnis |
| Organization name |
Washington University in Saint Louis
|
| Department |
Pathology and Immunology
|
| Lab |
Kipnis Lab
|
| Street address |
4515 McKinley Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE216388 |
Engineered T cell therapy for central nervous system injury [FACS-Tcells] |
| GSE216391 |
Engineered T cell therapy for central nervous system injury |
|
| Relations |
| BioSample |
SAMN31421808 |
| SRA |
SRX17999647 |
