|
| Status |
Public on Jul 01, 2024 |
| Title |
ctr.3R |
| Sample type |
SRA |
| |
|
| Source name |
right side region from sham animal
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cerebral
Sex: male
disease state: sham
time point: n/a
strain: C57BL/6
|
| Treatment protocol |
Mice were anesthetized and injected intraperitoneally with rose bengal (100 mg/kg) 5 min before laser irradiation by optic fiber centered 2 mm to skull right of the bregma. The brains were illuminated for 15 min (40mW output, 532nm from a 2mm diameter laser fiber), and the mice then recovered from anesthesia.
|
| Growth protocol |
Standard animal care
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The focal regions of cerebral ischemia were carefully micro-punched under a cryostat based on the location indicated by T2-weighted magnetic resonance images from the mouse with stroke after 4 hours, 1 day, 3 days, and 10 days (3 animals for sham animal and each time point). Three contralateral sham sides (left) of the mouse with stroke were randomly chosen as a left control group. The brain tissue with similar size at the right side region corresponding to the focal region in stroke mice were also punched from the sham mouse as a right control group. Punched tissue within each group (triplicate in 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 |
right side region from sham animal
|
| 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 Ballgown (ver. 2.5.3) timecourse comparison (with df=4) was performed to estimate the differential gene expression by the fragment per kilobase per million mapped reads (FPKM)
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (q value<0.05, FPKM and the differential expression data.)
|
| |
|
| Submission date |
Jul 05, 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) |
| GSE133897 |
Transcriptomic and proteomic multi-model global gene expression analysis reveals regulatory signatures during ischemia stroke (photothrombotic cerebral ischemia stroke) |
|
| Relations |
| BioSample |
SAMN12221298 |
| SRA |
SRX6409691 |
