|
| Status |
Public on Jul 01, 2024 |
| Title |
Ctr |
| Sample type |
SRA |
| |
|
| Source name |
left contralateral sham region
|
| Organism |
Mus musculus |
| Characteristics |
tissue: caudate putamen
disease state: sham
time point: n/a
strain: C57BL/6
|
| Treatment protocol |
After anesthetization with isoflurane gas, the mouse head was fixed using a small animal stereotactic frame. A scalp incision of 1 cm was made in the midline and a small hole was made on the skull above the caudate putamen (0.5 mm anterior to bregma, +/-2.5 mm lateral to midline). An unjacked optical fiber with 125 μm outer diameter and 50 μm core diameter was placed into a 28-gauge straight stainless steel needle. The other end of the optical fiber was connected to a 532 nm laser source (Shanghai Laser & Optics Century Co., Ltd, China). With the guidance of the needle, the optical fiber was stereotactically positioned to the caudate putamen (3 mm ventral to dura mater) in the mouse brain. 100 mg/kg rose bengal were then injected intraperitoneally (Sigma-Aldrich) 5 min before laser irradiation (another 2 min with 30mW output). On the sham side, all procedures were performed the same as above except applying the laser irradiation before rose bengal injection. After the scalp wound was secured, the mice were released from the stereotactic frame and transferred to a recovery chamber.
|
| Growth protocol |
Standard animal care
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mixed tissue of each group were then performed standard RNA extraction using Trizol
RNA-seq library construction according to the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd, Nanjing, China)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
The contralateral sham sides (left) of each mouse were also punched and mixed as control group
|
| Data processing |
Illumina HiSeq 2500 platform to get the raw data
Clean reads were generated from row reads by Trimmomatic (ver. 0.36) using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.90) with Hisat2 (ver. 2.1.0)
Mapped data were assembled by Stringtie (ver. 1.3.4d) with default parameters
Group comparison using GFold (ver. 1.1.4, sc=0.01) was performed to estimate the differential gene expression by the Reads per kilobase per million mapped reads (RPKM)
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (adjusted p value<0.01, RPKM, Gfold score, and the differential expression data.) RPKM also provided for all genes at all p-values.
|
| |
|
| Submission date |
Jul 10, 2019 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Sheng Zhao |
| E-mail(s) |
windupzs@outlook.com
|
| Organization name |
Southeast University
|
| Department |
Biochemistry and Molecular biology
|
| Lab |
Sheng Zhao's Lab
|
| Street address |
#87, Dingjiaqiao, Gulouqu
|
| City |
Not Hispanic or Latino |
| State/province |
N/A |
| ZIP/Postal code |
210009 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE134110 |
Transcriptomic and proteomic multi-model global gene expression analysis reveals regulatory signatures during ischemia stroke (photothrombotic internal ischemia stroke) |
|
| Relations |
| BioSample |
SAMN12250277 |
| SRA |
SRX6428958 |
