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| Status |
Public on May 17, 2024 |
| Title |
Ctrl_2 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
cell type: Astrocyte
genotype: Ctrl
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested usin RNeasy Lipid Tissue Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using vazyme TruePrep DNA Library Prep Kit following manufacturer’s protocol. 1 ng of total RNA was used for the construction of sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com/).
Structure variation detection The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5).
Assembly: mm10
Supplementary files format and content: tab-delimitated text file includes raw read and FPKM
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| Submission date |
Sep 06, 2023 |
| Last update date |
May 17, 2024 |
| Contact name |
Eiji Shigetomi |
| E-mail(s) |
[email protected]
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| Phone |
+81552739504
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| Organization name |
University of Yamanashi
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| Street address |
1110 Shimokato
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| City |
Chuo |
| State/province |
Yamanashi |
| ZIP/Postal code |
4093898 |
| Country |
Japan |
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| Platform ID |
GPL28457 |
| Series (1) |
| GSE242450 |
Disease-relevant upregulation of P2Y1 receptor in astrocytes enhances neuronal excitability via IGFBP2 |
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| Relations |
| BioSample |
SAMN37299462 |
| SRA |
SRX21645870 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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