|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|