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| Status |
Public on Nov 15, 2019 |
| Title |
p_stem_2 |
| Sample type |
SRA |
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| Source name |
p_stem
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| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate tumor
cell type: CD8 T-cell
cell subtype: Cd8+CD28+PD1+Tim3-
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Nov 14, 2019 |
| Last update date |
Nov 20, 2019 |
| Contact name |
Haydn Kissick |
| E-mail(s) |
haydn.kissick@emory.edu
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| Phone |
6172598364
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| Organization name |
Emory University
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| Street address |
1462 Clifton Rd
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| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE140430 |
Stem and effector CD8 T-cells from human cancers |
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| Relations |
| BioSample |
SAMN13288309 |
| SRA |
SRX7142042 |
| 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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