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Series GSE113741 Query DataSets for GSE113741
Status Public on May 10, 2018
Title Establishment and characterization of prostate cancer organoids [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease.
Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease.
We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.
Overall design To investigate the effects of organoid establishment on clonal selection and drift, we assessed patterns of gene expression from PDX and organoids from the same individual.

Total RNA was extracted from fresh organoids, using a Qiagen AllPrep DNA/RNA Mini Kit. RNA from each sample was quality checked using an Agilent TapeStation 2200 and RiboGreen Assay, and an aliquot of up to 3 micrograms of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility. After adaptor trimming, reads were simultaneously aligned to the hg19 genome (human) or mm10 genome (mouse) using Bowtie2 and Tophat version 2.1.1 without novel junction discovery, based on species-specific gene predictions downloaded from the UCSC genome table browser in January 2018. Each accepted-hits BAM file was sorted by read name and then processed by Disambiguate, which deposited species-specific read pairs into corresponding BAM files. Reads aligning equally well to both species' transcriptomes were discarded. The BAM file of reads preferentially aligning to the human transcriptome were processed by the PICARD SamToFastq tool to recover the FASTQ files, discarding all secondary alignments and singletons. The pre-processed data were then filtered to remove low quality reads, followed by the trimming of low quality bases. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count. Transcripts per million (TPM) were then normalized to the 75th percentile for each sample.

The FASTQ raw data for these samples are being submitted to dbGaP study phs001587 due to patient privacy concerns.

NIH grant(s):
ZIA BC011782 Mechanisms of Pathogenesis in Patient Derived Organoid Models of Prostate Cancer NATIONAL CANCER INSTITUTE KATHLEEN SIEBENLIST
ZIA BC011679 Mechanisms Driving Evolution of Aggressive Prostate Cancer NATIONAL CANCER INSTITUTE ADAM SOWALSKY
Contributor(s) Beshiri ML, Sowalsky AG, Corey E, Kelly K
Citation(s) 29748182
NIH grant(s)
Grant ID Grant title Affiliation Name
P50 CA097186 P-5: Maximal Targeted Inhibition of Androgen Signaling for Prostate Ca Therapy FRED HUTCHINSON CANCER RESEARCH CENTER PETER NELSON
Submission date Apr 27, 2018
Last update date Jun 14, 2019
Contact name Adam Sowalsky
Organization name National Cancer Institute
Department LGCP
Lab Sowalsky Lab
Street address 37 Convent Drive Building 37 Room 1062B
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (8)
GSM3118677 LuCaP_167_Organoid_Rep1
GSM3118678 LuCaP_167_Organoid_Rep2
GSM3118679 LuCaP_170.2_Organoid_Rep1
This SubSeries is part of SuperSeries:
GSE113743 Establishment and characterization of prostate cancer organoids
BioProject PRJNA453904

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113741_RAW.tar 1.5 Mb (http)(custom) TAR (of TXT)
Processed data provided as supplementary file
Raw data not provided for this record

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