|
| Status |
Public on Nov 23, 2021 |
| Title |
day14-TP+CNO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
transplanted human neural cells in the injured mouse spinal cord
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: neural cells differentiated from 414C2-iPS cell-derived neural stem/progenitor cells in the injured NOD-SCID mouse spinal cord, 14-days after the spinal cord injury.
treatment 1: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 9-days after the injury.
treatment 2: intraperitoneal injection of 5 mg/kg of CNO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The epicenter segmentsspinal cords were dissected in 4 mm-length and were rapidly frozen, and total RNA were isolated using NucleoSpin RNA/Protein (740933.50; Macherey-Nagel)
Total RNA from each sample was purified and mRNA libraries were prepared according to the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, United States) protocol and sequenced using NovaSeq 6000 (Illumina) to obtain 150-bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed based on the read quality and read length using Trim Galore version 0.6.6.
Mouse and human mRNA sequences were separated using Xenome version 1.0.0.
Separated RNA-seq data were mapped to the corresponding genomic DNA sequence (human GENCODE v34 and mouse GENCODE vM25) using Salmon version 1.4.0 with the default setting.
To obtain sufficient volume of human transcripts, the 42-days spinal cord RNAs were additionally sequenced to gain < 500 M reads of human transcripts. Human data were combined for further analyses.
Genome_build: human GENCODE v34 and mouse GENCODE vM25
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 24, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Momotaro Kawai |
| Phone |
81-3-5363-3812
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Orthopaedic Surgery
|
| Street address |
35 Shinanomachi
|
| City |
Shinjuku Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL25526 |
| Series (2) |
| GSE173244 |
Mouse spinal cords transplanted with human iPS cell-derived neural cells with and without chemogenetic stimulations on 14-days and 42-days after spinal cord injury. |
| GSE173245 |
Stimulation to human iPS cell derived neural stem/progenitor cells |
|
| Relations |
| BioSample |
SAMN18863873 |
| SRA |
SRX10674700 |
