Data · dataset · 2026
Raw transcriptome data of Mallard Bursa of Fabricius tissue
Listed in ScienceDB
Transcriptomics analysis aimed to investigate the changes in gene expression induced by PE-MPs exposure.
Description
The study randomly selected Bursa of Fabricius tissues from groups C (control group), L (1 mg/L), M (10 mg/L), and H (100 mg/L) after 6 weeks of PE-MPs treatment for transcriptomics analysis. Six biological replicates were set for each group.
Specifically, group C (C1, C2, C3, C4, C5, C6); group L (L1, L2, L3, L4, L5, L6); group M (M1, M2, M3, M4, M5, M6); and group H (H1, H2, H3, H4, H5, H6). After total RNA was extracted, RNA sequencing was performed using the Illumina NovaSeq X Plus Sequencing System (Illumina, Inc., San Diego, CA, USA). featureCounts (v2.0.6) was used to count the reads mapped to each gene. Then, FPKM for each gene was calculated based on gene length, and reads mapped to the gene were also counted.
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The DESeq2 R package (v1.42.0) was used for differential expression analysis between the two groups. The Benjamini-Hochberg method was used to adjust the resulting P-values to control the false discovery rate. The threshold for significant differential expression was set at |log2(FoldChange)| ≥ 1 and Padj < 0.05.
This sequencing completed transcriptomics analysis for a total of 24 samples, obtaining 174.31 Gb of clean bases. The clean bases for each sample reached more than 6.74 Gb, the percentage of Q20 bases was above 98.95%, and the percentage of Q30 bases was above 96.24%. The species name for this project was Anas_platyrhynchos.
The reference genome version was ncbi_anas_platyrhynchos_gcf_015476345_1_zju1_0. The reference genome sources were: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz, https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.gff.gz. The clean reads after quality control for each sample were quickly and accurately aligned to the reference genome to obtain the localization information of Reads on the reference genome.
The alignment rates for each sample ranged from 88.86% to 90.46%. A total of 17,133 expressed genes were detected in this analysis, including 16,447 known genes and 686 new genes.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.35780 ↗
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
- RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.35780 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| 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 |