|
| Status |
Public on Jul 27, 2019 |
| Title |
LuCaP_173-2A_ET2148_LCM_SCC |
| Sample type |
SRA |
| |
|
| Source name |
LuCaP 173.2 PDX tumor, LCM squamous pearl cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell line source: LuCaP
cell type: prostate cancer
sample type: LuCaP 173.2 PDX tumor
cell type: LCM squamous pearl cells
molecular phenotype: ARneg_NEneg
|
| Growth protocol |
LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from laser capture microdissected (LCM) LuCaP tumors with Arcturus PicoPure RNA Isolation Kit including the optional Dnase treatment.
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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LuCaP 173.2 PDX tumor, LCM squamous pearl cells
|
| 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
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X. For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
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).
|
| |
|
| Submission date |
Jul 26, 2019 |
| Last update date |
Jul 27, 2019 |
| Contact name |
Ilsa Coleman |
| E-mail(s) |
icoleman@fredhutch.org
|
| Phone |
206-667-1703
|
| Organization name |
Fred Hutchinson Cancer Center
|
| Department |
Human Biology
|
| Lab |
Peter Nelson
|
| Street address |
1100 Fairview Ave N, E2-112
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE126078 |
Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer |
|
| Relations |
| BioSample |
SAMN12369507 |
| SRA |
SRX6596822 |
