|
| Status |
Public on Jun 30, 2024 |
| Title |
hUC-MSCs, SCI rats in vivo, 1d, rep4 |
| Sample type |
SRA |
| |
|
| Source name |
human umbilical cord
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human umbilical cord
cell type: mesenchymal stem cells
treatment: intrathecal injection in subacute-SCI rats
time: Day 1
|
| Treatment protocol |
Human umbilical cord-derived MSCs were transplanted 2 week following SCI in rats. As controls, MSCs transplanted to the uninjured spinal cord and non-transplanted MSCs were used. At 1 day and 3 days post transplantation, the MSCs were isolated from the SCI and the sham。
|
| Growth protocol |
hUC-MSCs were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin-streptomycin, and 10 ng/ml recombinant human brain-derived neurotrophic factor (rhBDNF)， and maintained at 37C in a humidified incubator with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with TRIzol Reagent. Poly(A) RNA purified and used for library construction.
RNA libraries prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Five |
| |
|
| Description |
RS99
|
| Data processing |
Trimmomatic(v0.39) was employed to eliminate adapter sequences, poly-N sequences, and low_x0002_quality reads (quality scores below 30).
The filtered high-quality reads were aligned to the human reference genome (GRCh38) using the STAR aligner(v2.7.10) with default parameters.
Samtools(v1.16.1) was used to retain properly paired reads using the parameter “-f 4”.
gene expression levels were quantified via featureCounts (v2.0.3) using annotated gene models to generate raw read count data
Assembly: hg19
Supplementary files format and content: comma-separated values file includes raw counts for each Sample
Supplementary files format and content: comma-separated values file includes TPM values for each Sample
|
| |
|
| Submission date |
Dec 28, 2023 |
| Last update date |
Jun 30, 2024 |
| Contact name |
Mangmang Li |
| E-mail(s) |
mangmangli@smu.edu.cn
|
| Phone |
+86 13902289964
|
| Organization name |
Southern Medical University
|
| Department |
Department of Cell Biology School of Basic Medical Sciences
|
| Lab |
MM Lab
|
| Street address |
1838 N Guangzhou Ave
|
| City |
Guangzhou city |
| State/province |
Guangdong province |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL33758 |
| Series (1) |
| GSE252197 |
Neuroligin 3 promotes functional recovery of spinal cord injury through coordinating with Sar1a and Hspa8 at synapses |
|
| Relations |
| BioSample |
SAMN39181168 |
| SRA |
SRX23051275 |
