GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4161216 Query DataSets for GSM4161216
Status Public on Nov 15, 2019
Title B_Stem_4
Sample type SRA
Source name B_Stem
Organism Homo sapiens
Characteristics tissue: Bladder tumor
cell type: CD8 T-cell
cell subtype: Cd8+CD28+PD1+Tim3-
Extracted molecule total RNA
Extraction protocol RNA and DNA was extracted using qiagen all-prep kits
DNA methylation was done using illumina methylseq protocol, Bladder rna libraries were prepared using Nugen Ovation, Kidney and prostate RNA libraries prepared using clontech smartseq V2
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Rna samples: Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2
DNA methylation: Adapter trim with cutadapt, differentially methylated CpGs identified by fisher exact test compared to each CpGs Naïve cells, Differentially methylated regions identified using custom python analysis finding continuous regions with atleast 5/10 significantly (p=0.0001) differentially methylated CpGs
Genome_build: hg38
Supplementary_files_format_and_content: Counts
Submission date Nov 14, 2019
Last update date Nov 20, 2019
Contact name Haydn Kissick
Phone 6172598364
Organization name Emory University
Street address 1462 Clifton Rd
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
Platform ID GPL21290
Series (1)
GSE140430 Stem and effector CD8 T-cells from human cancers
BioSample SAMN13288319
SRA SRX7142032

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap