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| Status |
Public on Jul 04, 2024 |
| Title |
CD8_WT_2 |
| Sample type |
SRA |
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| Source name |
CD8 T cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: CD8 T cells
cell type: CD8 T cell
genotype: WT
strain: C57Bl/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from murine T cells via RNeasy Kit (Qiagen) with DNase digestion (Qiagen) following manufacturer’s instructions.
Total RNA was reverse transcribed using a High-Capacity cDNA Reverse Transcriptase kit (Life Technologies). RNA preparation and library construction for RNA sequencing was conducted by the VAI Genomics Core as previously described(Roy et al., 2020).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample_3
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| Data processing |
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0).
Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8).
Counts were then normalized and differential expression was calculated using DESeq2.
Gene-set enrichment analysis (GSEA) on RNA-seq data was conducted using the gage function and non-parametric Kolmogorov–Smirnov test from the GAGE (version 2.22.0) R Bioconductor package(Luo et al., 2009).
Assembly: mm10
Supplementary files format and content: 20220203 ACLY in vivo RNAseq.xlsx is an excel file containing differential gene expression, pathway and geneset enrichment analysis.
Supplementary files format and content: Normalized_cpm.txt contains normalized counts per million transcripts for each sample.
Supplementary files format and content: raw_counts_7samples_filtered.txt contains raw non-normalized counts of transcripts for each sample.
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| Submission date |
Jun 26, 2024 |
| Last update date |
Jul 04, 2024 |
| Contact name |
Brandon Oswald |
| E-mail(s) |
Brandon.Oswald@vai.org
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| Phone |
6168343380
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| Organization name |
Van Andel Institute
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| Department |
Metabolism
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| Lab |
Russell Jones
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| Street address |
333 Bostwick Ave NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE270851 |
ACLY and ACSS2 link nutrient-dependent chromatin accessibility to regulation of CD8 T cell effector responses [RNA-seq] |
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| Relations |
| BioSample |
SAMN42072193 |
| SRA |
SRX25069607 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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