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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 11, 2023 |
| Title |
CON3 |
| Sample type |
SRA |
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| Source name |
prostate
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| Organism |
Mus musculus |
| Characteristics |
tissue: prostate
Sex: male
cell type: mouse anterior prostatic cells
genotype: Wild type
age: 20 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Anterior prostates from 20-week-old male mice for RNA-Seq analysis (the prostatic secretions must be cleaned otherwise RNA quality was poor）. Using the Trizol RNA Reagent (Takara, Dalian, China) to extract total RNA from the tissues and measured the concentration and integrity of the RNA with the ND-1000 Nanodrop, as well as the Agilent 2100 TapeStation (Novogene Bioinformatic Technology, Beijing, China). The quality control parameters used in this study were: A260/A280 ratio ≥1.8, A260/A230 ratio ≥2.0, and RNA integrity number ≥8.0.
The TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) was used to generate cDNA libraries. High-throughput sequencing was run on an Illumina HiSeq 2500 system. Raw RNA-seq data were processed with an in-house computational pipeline.
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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 |
featureCounts v 1.5.0-p3 and stringtie v 1.3.3b
Initial quantification was performed using Qubit2.0 Fluorometer, followed by Agilent 2100 BioAnalyzer testing the insert size of the library. When the insert size met expectations, Qrt-pcr accurately quantified effective library concentration (effective library concentration is higher than 2nM) to ensure library quality.
The image data measured by the high-throughput sequencer were converted into sequence data (reads) by CASAVA base recognition.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Apr 11, 2022 |
| Last update date |
Apr 12, 2023 |
| Contact name |
Ren-Wei Su |
| E-mail(s) |
[email protected]
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| Organization name |
South China Agricultural University
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| Department |
Histology and Embryology
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| Lab |
Su' Lab
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| Street address |
483 Wushan Road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE200565 |
Aberrant activation of canonical Notch1 signaling in the mouse prostate drives epithelialcell proliferation and induces prostatic hyperplasiaby increasing androgen receptor sensitivity |
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| Relations |
| BioSample |
SAMN27512766 |
| SRA |
SRX14809859 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6037860_CON3.txt.gz |
315.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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