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Sample GSM7763673 Query DataSets for GSM7763673
Status Public on May 17, 2024
Title AstroP2Y1OE_1
Sample type SRA
 
Source name Hippocampus
Organism Mus musculus
Characteristics tissue: Hippocampus
cell type: Astrocyte
genotype: AstroP2Y1OE
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
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
 
Submission date Sep 06, 2023
Last update date May 17, 2024
Contact name Eiji Shigetomi
E-mail(s) eshigetomi@yamanashi.ac.jp
Phone +81552739504
Organization name University of Yamanashi
Street address 1110 Shimokato
City Chuo
State/province Yamanashi
ZIP/Postal code 4093898
Country Japan
 
Platform ID GPL28457
Series (1)
GSE242450 Reactive astrocytes enhance neuronal excitability via IGFBP2: pathological effects of P2Y1 receptor upregulation
Relations
BioSample SAMN37299460
SRA SRX21645872

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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