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| Status |
Public on Mar 11, 2026 |
| Title |
RNA-seq of peripheral blood in HTRA3-associated cerebral small vessel disease |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
group: HTRA1mc
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by the chloroform method.
Total RNA was used as the starting material for library construction. After enrichment of the extracted total RNA, the poly-A–tailed mRNA was randomly fragmented by adding buffer. Using the fragmented mRNA as template and random oligonucleotides as primers, the first-strand cDNA was synthesized, followed by the second-strand cDNA synthesis with dNTPs. The purified double-stranded cDNA was subjected to end repair, A-tailing and ligation of sequencing adapters, followed by PCR amplification and purification of PCR products, and the sequencing library was finally constructed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Library name: sample3
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| Data processing |
Reference genome index was constructed using HISAT2 v2.0.5, and paired-end clean reads were aligned to the reference genome. Feature Counts (1.5.0-p3) was used to count the reads mapped to each gene, and the gene expression levels were quantified by Fragments Per Kilobase of transcript per Million mapped reads (FPKM). After the image data generated by the high-throughput sequencer was processed for base calling using CASAVA software, it was converted into sequence data (reads). To ensure the quality and reliability of data analysis, raw data was filtered, including removing reads with adapter sequences, reads containing ambiguous base information, and low-quality reads (the number of bases with Qphred ≤ 5 accounting for more than 50% of the entire read length).
Assembly: hg38
Supplementary files format and content: TXT file including Reads count for each sample.
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| Submission date |
Mar 06, 2026 |
| Last update date |
Mar 11, 2026 |
| Contact name |
Shina Song |
| E-mail(s) |
snpp1024520@126.com
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| Organization name |
The First Hospital of Shanxi Medical University
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| Street address |
Jiefangnan 85 Road
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| City |
Shanxi |
| ZIP/Postal code |
030001 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE324041 |
HTRA1 Mutation and Expression Regulation in Cerebral Small Vessel Disease |
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| Relations |
| BioSample |
SAMN56360361 |
| SRA |
SRX32395438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM9567281_HTRA1mc3.txt.gz |
251.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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