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| Status |
Public on Nov 07, 2021 |
| Title |
Enzalutamide_7 |
| Sample type |
SRA |
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| Source name |
PC346C-DCC-K xenograft
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
condition: Prostate cancer
gender: male
mouse model: NMRI nu/nu
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| Treatment protocol |
Daily oral administration of Enzalutamide (60/mg/kg) or placebo control (vehicle of 1% w/v carboxymethylcellulosesodium salt, with 0.1% v/v Tween 80). Treatment started when xenograft tumors surpassed a volume of 150 mm3 and lasted 7 days.
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| Growth protocol |
Twenty-one, six weeks old, NMRI nu/nu male mice (Janvier, Le Genest Saint Isle, France) were subcutaneously inoculated with 5*10E6 PC346C-DCC-K cells. Tumor growth was observed after 2-5 weeks in ~80% of the mice.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumor tissue was lysed and homogenized in QIAzol (ref #79306, Qiagen, Hilden, Germany) using an Ultra-Turrax T25 (Janke & Kunkel, Staufen, Germany). Total RNA was isolated using the miRNA-easy mini kit (ref # 217004, Qiagen), and RNA quality was measured using the Bioanalyzer RNA 6000 Nano assay (ref #5067, Agilent, Santa Clara, California, USA). All RNA samples had a RIN value ≥7.
Library Prep was performed using the NEBNext Ultra Directional RNA Kit for Illumina according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L).
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After mRNA fragmentation, cDNA synthesis was performed and used for ligation with adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. One sample was re-sequenced due high frequency of multi-mapped reads implicating inadequate depletion of ribosomal RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
FASTQC v0.11.5
trimmomatic v0.36
STAR v2.5.3a
AstraZeneca’s disambiguation algorithm Python variant, 2013
sambamba Flagstat v0.6.7
FeatureCounts v1.5.2
DESeq2 package v1.18.1
Genome_build: hg38
Genome_build: mm10
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| Submission date |
Oct 08, 2021 |
| Last update date |
Nov 07, 2021 |
| Contact name |
Lisanne Mout |
| E-mail(s) |
lisanne.mout@uhnresearch.ca
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| Organization name |
University Health Network
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| Street address |
101 College st
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| City |
Toronto |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
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| Platform ID |
GPL25431 |
| Series (1) |
| GSE185587 |
Differential gene expression induced by Enzalutamide in a prostate cancer xenograft |
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| Relations |
| BioSample |
SAMN22165515 |
| SRA |
SRX12539370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5619034_103382-001-010.markdup.fcnt.txt.gz |
4.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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