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| Status |
Public on Feb 01, 2019 |
| Title |
NP_22 |
| Sample type |
SRA |
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| Source name |
CD8+ T cell IL-7RαloKLRG1hi
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8+ T cell IL-7R{alpha}loKLRG1hi
donor: F
tissue: Blood
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy mini kit
NEBNext Ultra Directional RNA Library Prep Kit for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17
Alignment of reads was done using STAR (v2.4.0j)
For each gene all reads were counted that aligned to exonic regions using featureCounts (v1.4.3-p1) with Homo_sapiens.GRCh38.87.gtf annotation from Ensembl
Differentially expression analysis was done in R limma trend (v2.13.0), taking the donor as batch factor in the model. Genes with less than 1 CPM in 3 or more samples were removed from further analysis. Groups (cell type) were compared in contrasts and genes with an FDR-adjusted p-value < 0.05 were considered significant.
Genome_build: hg38
Supplementary_files_format_and_content: Raw read count per gene
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| Submission date |
Apr 13, 2018 |
| Last update date |
Feb 01, 2019 |
| Contact name |
Benjamin Nota |
| E-mail(s) |
benjamin.nota@gmail.com
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| Phone |
+31 (0)20-5123787
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| Organization name |
Sanquin
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| Department |
Research Facilities
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| Street address |
Plesmanlaan 125
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| City |
Amsterdam |
| State/province |
Noord Holland |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE113098 |
Functional separation of IL7Rα/KLRG1-defined CD8+ T cell populations in humans |
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| Relations |
| BioSample |
SAMN08925003 |
| SRA |
SRX3932288 |
| 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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