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| Status |
Public on Sep 16, 2024 |
| Title |
WT7, control |
| Sample type |
SRA |
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| Source name |
intestine
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| Organism |
Danio rerio |
| Characteristics |
tissue: intestine
cell type: leukocyte
genotype: Wildtype
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from wild-type or ctla-4-/- intestines (three biological replicates) using TRIzol reagent following the manufacturer's instructions (Takara).
cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit (NEB), and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio (Hangzhou, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The differentially expressed genes (DEGs) were identified with absolute Log2 fold change > 1 and adjusted p-value < 0.05 by R package DESeq2. Gene Ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed by the OmicStudio (http://www.omicstudio.cn/tool) tools. Gene-set enrichment analysis was performed using software GSEA (v4.1.0, https://www.gsea-msigdb.org/gsea/index.jsp), and the heatmap was generated using the R package ggplot2. For the protein-protein interaction (PPI) networks, the DEGs were retrieved in STRING (version 11.5, https://string-db.org/) database (combined score > 0.4), and the PPI network was visualized by Cytoscape software (version 3.9.1)6. The betweenness centrality (BC) was calculated using the CytoNCA plugin in Cytoscape software.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Feb 07, 2024 |
| Last update date |
Sep 16, 2024 |
| Contact name |
Qin Lu lu |
| E-mail(s) |
12007075@zju.edu.cn
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| Organization name |
zhejiang university
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| Street address |
Gudun Road, Xihu District
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL18413 |
| Series (1) |
| GSE255304 |
Ctla-4 deficiency induces an inflammatory bowel disease-like phenotype in a zebrafish model [bulkRNA-seq] |
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| Relations |
| BioSample |
SAMN39860323 |
| SRA |
SRX23567382 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8068835_WT7.xlsx |
1.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
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