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Sample GSM5173906 Query DataSets for GSM5173906
Status Public on Apr 14, 2021
Title SAßGal low, old donor #3
Sample type SRA
Source name CD8+ T Cells
Organism Homo sapiens
Characteristics saßgal activity: Low
cell type: CD8+ T Cells
age: old
Treatment protocol Young and old donors were always processed in pairs to allow for direct comparison
Growth protocol Blood was isolated from healthy donors in their 20`s and 60's, PBMCs isolated by density centrifugation and CD8+ T cells enriched by negative selection using a StemCell EasySep Human CD8+ T‐Cell Isolation Kit
Extracted molecule total RNA
Extraction protocol Macherey-Nagel RNA-XS kit
Smarted Stranded V2 Kit (Takara)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Base Calling was performed with RTA version 2.0
Alignment was performed with bowtie2 using the local option against the hg19 version of the human genome
Reads in exons were counted with SummarizeOverlaps, using exons from Homo_sapiens.GRCh37.75.gtf
Reads were filtered as follows: at least 3 samples have at least 5 reads per every gene
Read normalization was performed during differential analysis with DESeq2. For visualizations, we used rld-transformed reads.
Differentially expressed genes were clustered with WGCNA, with two gene modules being identified.
Genome_build: hg19
Supplementary_files_format_and_content: counts per exon; rld transform and log2 fold-change of differentially expressed genes
Supplementary_files_format_and_content: raw counts and rld transformed values per gene (SummarizeOverlaps and DESeq2 rld transform output)
Supplementary_files_format_and_content: rld transformed values and log2 fold change of differentially regulated genes (DESeq2 output)
Submission date Mar 16, 2021
Last update date Apr 14, 2021
Contact name Ricardo Iván Martínez Zamudio
Organization name Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School
Department Pharmacology
Lab Martínez Zamudio Lab
Street address 675 Hoes Lane West
City Piscataway
State/province New Jersey
ZIP/Postal code 08854
Country USA
Platform ID GPL24676
Series (1)
GSE169009 Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans
BioSample SAMN18320281
SRA SRX10355050

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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