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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 16, 2019 |
| Title |
4_1546_5-1_35CR-ENZR_SPT_EOS |
| Sample type |
SRA |
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| Source name |
LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 4_1546_5-1
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
tumor type: LuCaP 35CR-ENZR tumor
treatment group: Supraphysiological testosterone (SPT)
timepoint: End of Study (EOS)
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| Treatment protocol |
When the tumor reached 40-100 mm3, mice started ENZ (MedChem Express, TX; 50 mg/kg in PBS containing 1% CMC/0.1% Tween-80/5% DMSO) by oral gavage daily, 5 days on 2 days off a week. When ENZ resistance developed (i.e. after 1 week for LuCaP 35CR and 2 weeks for LuCaP 96CR and LuCaP 77CR), mice were randomized to control or SPT treatment groups; Fig. 2A). Tumor volume and body weight were measured twice weekly, and blood samples were drawn weekly for PSA measurements using Architect Total PSA Assay (Abbott Laboratories, Abbott Park, IL). Five animals in each group were sacrificed 5 days after the initiation of treatment (D5) and the remaining animals were followed and sacrificed when tumors exceeded 1,000 mm3 or after 8 weeks, whichever came earlier (end of study, EOS) or sacrificed if animals became compromised. At sacrifice (D5 or EOS), tumors were harvested for paraffin embedding and frozen for subsequent analyses.
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| Growth protocol |
Male CB-17 SCID mice (aged 6-8 weeks; Charles River Laboratories, San Diego, CA) were castrated and two weeks later implanted subcutaneously with LuCaP 35CR, LuCaP 96CR, or LuCaP 77CR tumor bits.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNA STAT 60 (Tel-Test, Friendswood, TX) and RNeasy Mini kit, followed by DNase digestion in solution prior to purification (Qiagen, Germantown, MD) for RNA-seq and quantitative PCR analyses. RNA integrity number was determined using the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq 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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| Data processing |
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.64.0 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 and mm10 mouse genomes using TopHat v2.1.0. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.) If samples were sequenced more than once, the human filtered bam files were combined prior to further analysis.
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 v1.12.0 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: *_processed_data.txt: 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 |
Jan 06, 2019 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Ilsa Coleman |
| E-mail(s) |
[email protected]
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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) |
| GSE124704 |
Durable Response of Enzalutamide-resistant Prostate Cancer to Supraphysiological Testosterone Is Associated with a Multifaceted Growth Suppression and Impaired DNA Damage Response Transcriptomic Program in Patient-derived Xenografts |
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| Relations |
| BioSample |
SAMN10697333 |
| SRA |
SRX5209733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3543641_4_1546_5-1_processed_data.txt.gz |
690.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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