Data · dataset · 2024
Transcriptome differential gene dataset of low-density neutrophils and normal-density neutrophils in peripheral blood of patients with Sporotrichosis
Listed in ScienceDB
Total RNA was extracted from both NDNs and LDNs using TRIzol reagent, in accordance with the manufacturer’s instructions (Trans Gen, Beijing, China).
Description
RNA concentration and quality were assessed using a microplate reader (Synergy HTX, BioTek). RNA samples were then submitted to BGI Service Co., Ltd.
(service ID #F23A040014029, Wuhan, China) for RNA sequencing and subsequent bioinformatics analysis. Raw sequencing data were filtered using SOAPnuke software (v1.5.6) to obtain clean reads. These clean reads were aligned to the reference genome using HISAT2 software (v2.1.0).
Read the rest (2 more)
The Dr. Tom System from BGI (biosys.bgi.com) was used for data analysis, plotting, and mining. DEGs were identified using FDR-adjusted q-values < 0.05 and fold changes > 2.
To elucidate the functional implications of DEGs, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed with the Dr. Tom System; results were visualized using a bubble diagram. GSEA was performed using KEGG gene sets, with significance defined as a NES ≥ 1.0, a nominal p-value < 0.05, and an FDR-adjusted q-value ≤ 0.25.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.11160 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Genetics 69% · RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.11160 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3105 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (69%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |