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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2021 |
| Title |
Thy CD8 WT_2 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: T cells
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were harvested from fresh tissues according to standard procedures and surface-stained in FACS buffer with monoclonal antibodies. Related T cell subsets from mice spleen or thymus were sorted with FACS Aria II Cell Sorter. For bulk RNA-seq, total RNA was extracted from tissue by Trizol reagent.
For bulk RNA-seq, complementary DNA (cDNA) libraries were prepared using the NEBNextTM Ultra Directional RNA Library Prep Kit, NEBNext Poly (A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos according to the manufacturer’s instructions. The products were purified and enriched by PCR to create the final cDNA libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
counts_thy_CD8.txt
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| Data processing |
For RNA-Seq, before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to the mouse genome (GRCm38) using Hisat2. HTseq was used to obtain gene counts, and the RPKM method was used to determine gene expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: For RNA-Seq, Matrix table with raw gene counts for every gene and every sample.
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| Submission date |
Oct 29, 2021 |
| Last update date |
Nov 01, 2021 |
| Contact name |
zheyi chen |
| E-mail(s) |
[email protected], [email protected]
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| Organization name |
Shanghai Jiao Tong University School of Medicine
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| Street address |
1665 Kong Jiang Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE186851 |
PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells [RNA-seq] |
| GSE186863 |
PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells |
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| Relations |
| BioSample |
SAMN22786297 |
| SRA |
SRX12839223 |
| 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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