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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 30, 2024 |
| Title |
KO_Ctl, rep 3, RNAseq |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: NK cells
genotype: KO
treatment: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by miRNeasy Micro kit (QIAGEN).
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s instructions.
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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 |
Quality control of sequenced reads was assessed by FastQC (version 0.11.9).
Sequencing reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.8a). Aligned reads were counted using summarizeOverlaps from the GenomicAlignments Bioconductor package.
Counts were loaded into R and analyzed with the edgeR and limma packages. Genes were filtered to have at least 10 CPMs (counts per million) in two samples.
Library normalization factors were computed with the TMM method. A design matrix was used containing a group variable composed of the background (WT or KO) or stimulus (Ctl or Sti) status. The voom method implemented in the limma package was used with this design matrix to estimate the mean variance trend.
A linear model was fitted with lmFit function.
Assembly: mm10
Supplementary files format and content: count.rds
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| Submission date |
Jul 18, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
Xin Sun |
| E-mail(s) |
sunxin@ifrec.osaka-u.ac.jp
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| Organization name |
IFReC, Osaka University
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| Street address |
3-1 Yamadaoka, Suita
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| City |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE237641 |
The transcriptional landscape associated with the deletion of Regnase-1 [RNA-Seq] |
| GSE237643 |
Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2- dependent transcription of Ifng |
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| Relations |
| BioSample |
SAMN36536405 |
| SRA |
SRX21075971 |
| 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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