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| Status |
Public on Jul 24, 2024 |
| Title |
Control, replicant 2 [miRNA] |
| Sample type |
SRA |
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| Source name |
Hypertrophic scars
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: Hypertrophic scars
Sex: female
breed: New Zealand White
treatment: Treated with saline for 21 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, total RNA was extracted from samples with an achieved yield of 1 µg per sample. Integrity and purity were confirmed using agarose gel electrophoresis (28S:18S ≥ 1.5) and Nanodrop spectrophotometry (OD260/280 ratio between 1.8 and 2.2), respectively. RNA concentration was quantified using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Inc.), with minimum readings of 500 ng/µl.
Adaptors were added to both ends of small RNAs, and cDNA was synthesized through reverse transcription, followed by purificatiox n using QIAseq miRNA NGS Beads (cat. no., 333923; Qiagen).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample A2
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| Data processing |
Quality control of the raw sequencing reads is performed using FastQC (version 1.0.0) to ensure data integrity. Low-quality bases and adapter sequences are then removed from the reads using trimming tools Trimmomatic (version 0.40). The high-quality reads are aligned to transcriptome with aligners STAR (version 2.7.6a). The aligned reads are stored in BAM files, which are then sorted, indexed, and processed to mark duplicate reads and generate alignment statistics. Gene and transcript expression levels are quantified from the aligned reads using tools HTSeq (version 2.0.3). The expression data are normalized to account for technical variations, and differential expression analysis is conducted using DESeq2 (version 1.30.1) to identify genes with significant expression changes between experimental conditions.
Assembly: OryCun3.0
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jul 08, 2024 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Lijun Hao |
| E-mail(s) |
lijunhao@hrbmu.edu.cn
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| Organization name |
the First Affiliated Hospital of Harbin Medical University
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| Street address |
23 Youzheng Street
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| City |
Harbin |
| ZIP/Postal code |
150000 |
| Country |
China |
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| Platform ID |
GPL26786 |
| Series (1) |
| GSE271672 |
Exosomal miR-194 from adipose-derived stem cells impedes hypertrophic scar formation through targeting TGF-β1 [miRNA] |
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| Relations |
| BioSample |
SAMN42360811 |
| SRA |
SRX25234044 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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