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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 17, 2019 |
| Title |
CRPC_17-033J1_PANCREAS |
| Sample type |
SRA |
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| Source name |
CRPC pancreas metastasis
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell type: prostate cancer
tumor site: pancreas
patient: 17-033
molecular phenotype: ARpos_NEpos
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 98 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 55 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from flash frozen LuCaP xenograft tissue or cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CRPC pancreas metastasis
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| Data processing |
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).
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| Submission date |
Feb 04, 2019 |
| Last update date |
Mar 20, 2020 |
| Contact name |
Ilsa Coleman |
| E-mail(s) |
icoleman@fredhutch.org
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| Phone |
206-667-1703
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| Organization name |
Fred Hutchinson Cancer Center
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| Department |
Human Biology
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| Lab |
Peter Nelson
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| Street address |
1100 Fairview Ave N, E2-112
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE126078 |
Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer |
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| Relations |
| Reanalyzed by |
GSM4422745 |
| BioSample |
SAMN10871117 |
| SRA |
SRX5331984 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3591106_17-033J1_PANCREAS_processed_data.txt.gz |
713.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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