|
| Status |
Public on May 11, 2020 |
| Title |
T9I3 |
| Sample type |
SRA |
| |
|
| Source name |
Spinal cord
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: 5 days-post injury
tissue: T9 spinal cord
strain: Sprague Dawley
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords were removed, flash frozen in liquid nitrogen, and RNA was harvested using NucleoSpin® RNA XS (TaKaRa).
Libraries were constructed by using CEL-Seq2 protocol.
RNA-Seq (3' tag-Seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
1N-3
|
| Data processing |
The raw sequence reads were aligned to the rat reference genome (Rnor_6.0) using HISAT2 (version 2.0.4).
Read counting was performed with HTSeq (version 0.6.0) so that UMI duplicates were removed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The txt file contains UMI count matrix.
|
| |
|
| Submission date |
Oct 09, 2019 |
| Last update date |
May 11, 2020 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
|
| Organization name |
Medical Institute of Bioregulation
|
| Lab |
Division of Transcriptomics
|
| Street address |
3-1-1 Maidashi
|
| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18404 |
| Series (1) |
| GSE138637 |
Genome wide analysis of thoracic spinal cord at 5 days after T9 hemisection injury. |
|
| Relations |
| BioSample |
SAMN13000143 |
| SRA |
SRX6969532 |
