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| Status |
Public on Jul 02, 2024 |
| Title |
WT_spleen_rep2 |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD4+ YFP+ Treg
genotype: Foxp3YFPCre/+ Tfrc+/+
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Single Cell RNA Purification Kit (Norgen) following the manufacturer’s protocol.
RNA-Seq library for mRNA sequencing was prepared with SMARTer Stranded Total RNA-Seq kit - Pico Input Mammalian. All extracted RNA samples were quality controlled for integrity with a 2100 Bioanalyzer system (Agilent Technologies) and were sequenced on a NovaSeq 6000 System (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter using the auto detection mode and the following parameters: --clip_r1 3 --three_prime_clip_r2 3.
Then reads were mapped to the mouse Ensembl GRCm38 transcriptome index using salmon (v.1.3.0).
Gene-level normalization and differential gene expression analysis were performed with Bioconductor (Gentleman et al., 2004; Huber et al., 2015) package DESeq2 v.1.28 (Love et al., 2014) using the R environment v.4.0 (R Core Team, 2015).
The Wald test was used for significance testing and the resulting false discovery rate (FDR) p-values were adjusted for multiple comparisons using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) and genes were considered differentially expressed (DEGs) only at FDR < 0.05
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample
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| Submission date |
Sep 04, 2022 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Valerio Licursi |
| E-mail(s) |
valerio.licursi@uniroma1.it
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| Organization name |
Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)
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| Department |
c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome
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| Street address |
via degli Apuli, 4
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| City |
Rome |
| ZIP/Postal code |
00185 |
| Country |
Italy |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE212688 |
Iron capture through CD71 dictates perinatal and tumoral Treg expansion modulating iron homeostasis and gut microbiota colonization |
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| Relations |
| BioSample |
SAMN30671291 |
| SRA |
SRX17424767 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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