Data · dataset · 2025
RNA-Seq analysis
Listed in Teesside University Research Data Repository
The obtained cDNA library was then sequenced on the Illumina platform.
Description
The raw data was filtered using Trimmomatic, resulting in clean data. Reads were aligned to the reference genome with HISAT2 (version: 2.2.1).
For three biological replicates, DESeq2 (version: 1.34.0) was used to identify differentially expressed genes, while edgeR (version: 3.36.0, dispersion = 0.01) was applied for datasets without replicates. We first selected differentially expressed genes with a Fold Change ≥ 2 and FDR < 0.05. If the number of differentially expressed genes in each comparison group exceeded 1,000, we tightened the selection criteria to Fold Change ≥ 2 and FDR < 0.01.
Read the rest (2 more)
In this analysis, we ultimately chose to filter differentially expressed genes with an FDR < 0.01. Differentially expressed genes and samples were clustered using the R package Pheatmap. StringTie was used to map reads, assemble transcripts, and compare them with known genes using Cuffcompare.
Differential splicing was analyzed with rMATS. Finally, Samtools aligned the sorted, PCR-deduplicated files with the reference sequence to detect variants. In the analysis data, abbreviation "B" represents BTZ treatment, and "CB" represents CURE treatment.
Links
Where it is published
- DOI doi.org/10.17632/jjrp3mmf24.1 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Nanomedicine · Social Science
- Inferred from text
- RNA sequencing 65%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/jjrp3mmf24.1 | 4 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].anzsrc:field:320604 | mapping · researchdata tees ac uk | vocabulary-mapper@1.0.0 | keywords['Nanomedicine'] |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · researchdata tees ac uk | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |