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| Status |
Public on Apr 01, 2024 |
| Title |
D5brain,Minocycline |
| Sample type |
SRA |
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| Source name |
Paraventricular hypothalamic nucleus
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Paraventricular hypothalamic nucleus
genotype: WT
treatment: Minocycline treatment and immobilized stress
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
D5brain
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| Data processing |
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Assembly Rnor6.0
Supplementary files format and content: gene_fpkm.txt
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| Submission date |
Mar 18, 2024 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Bin Li |
| E-mail(s) |
binli1996@outlook.com
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| Organization name |
First Affiliated Hospital of Harbin Medical University
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| Department |
Department of Cardiology
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| Street address |
No. 23, Postal Street, Nangang District
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| City |
Harbin |
| State/province |
Heilongjiang |
| ZIP/Postal code |
150001 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (1) |
| GSE261833 |
Role of hypothalamic microglial activation on ventricular arrhythmias in stress cardiomyopathy |
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| Relations |
| BioSample |
SAMN40529852 |
| SRA |
SRX23986065 |
| 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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