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Sample GSM5906830 Query DataSets for GSM5906830
Status Public on Feb 08, 2023
Title H_KA_2
Sample type SRA
 
Source name Brain
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: KA-induced TLE model
treatment: Treated with KA
Extracted molecule total RNA
Extraction protocol Brain were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description KA_mouse.txt
Data processing Illumina Casava1.7 software used for basecalling.
sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
clean reads were separately aligned to reference genome with orientation mode using the HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Genome_build: mm10
 
Submission date Feb 18, 2022
Last update date Feb 08, 2023
Contact name Dijun Chen
E-mail(s) dijunchen@nju.edu.cn
Organization name Nanjing University
Department Life Sciences
Street address Xianlin
City Nanjing
State/province Jiangsu
ZIP/Postal code 310028
Country China
 
Platform ID GPL24247
Series (2)
GSE190453 Lipid-accumulated reactive astrocytes promote seizure activity in epilepsy
GSE197015 Lipid-accumulated reactive astrocytes promote seizure activity in epilepsy [mouse]
Relations
BioSample SAMN26084461
SRA SRX14224181

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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