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| Status |
Public on Feb 07, 2019 |
| Title |
Sample_PC3plus |
| Sample type |
SRA |
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| Source name |
PC-3
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| Organism |
Homo sapiens |
| Characteristics |
rnase r treatment: yes
treatment: N/A
cell line: PC-3
cell type: prostate cancer cell line
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| Growth protocol |
The four PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin. LNCaP cells were serum starved for 48 hours before stimulation with 10 nM double hydrogen testosterone (DHT) for 4 or 16 hours.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For the preparation of the RNA-Seq libraries for the four cell lines, 10 µg of total RNA was subjected to RiboMinus for the removal of the ribosomal RNA by using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K155001). After RiboMinus treatment, the samples (~1 µg left) were divided into two equal portions, one treated with RNase R and the other incubated only with the digestion buffer. Samples were cleaned-up by phenol-chloroform before resuspension in a small volume of RNase-free H2O.
he library preparation commenced directly with the fragmentation step by mixing the sample and the Fragment, Prime, Finish Mix in the TruSeq Stranded mRNA Library Prep Kit at a 1:1 ratio, followed by the manufacturer’s protocol for the remainder of the procedure. RNA-Seq libraries were sequenced as single-end reads in duplicates at ~50 million reads per library using HiSeq 2000 platforms.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 6
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| Data processing |
RNA-Seq reads were mapped to GRCh37 with Gencode v24lift37 annotation using STAR (v2.5.3a), the GeneCounts parameter was set to quantMode to get raw counts on genes
RNA-Seq reads were mapped to GRCh37 using Tophat v2.1.0 with Gencode v24lift37 annotations. Unaligned reads were converted to fastq format with bamToFastq function from the Bedtools suite and used to call fusion with TopHat-Fusion v2.1.0, with anchor length set as 20 bp. The resulting fusion reads were annotated with CIRCexplorer v1.1.10.
edgeR(v3.12.1) was used to obtain FPKM
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for gene raw counts and reads encompassing back-splicing site for circRNAs
Supplementary_files_format_and_content: circRNA_RPKM_CPC.csv: comma-separated text file; circRNA RPKM for CPCGENE dataset.
Supplementary_files_format_and_content: circRNA_RPKM_NGS.csv: comma-separated text file; circRNA RPKM for NGS-ProToCol dataset.
Supplementary_files_format_and_content: circRNA_annotation.csv: comma-separated text file; circRNA annotation.
Supplementary_files_format_and_content: circRNA_RPKM_circRNA_RPKM_cpc144_patient.csv: comma-separated text file; RPKM for all circRNAs detected in CPCGENE cohort.
Supplementary_files_format_and_content: circRNA_annotation_76311.csv: comma-separated text file; circRNA annotation.
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| Submission date |
Apr 13, 2018 |
| Last update date |
Oct 27, 2020 |
| Contact name |
Housheng Hansen He |
| E-mail(s) |
[email protected]
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| Organization name |
University of Toronto
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| Lab |
He lab
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| Street address |
101 College Street
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE113120 |
RNA-Seq with and without RNase treatment in PCa cell lines |
| GSE113124 |
Widespread and Functional RNA Circularization in Localized Prostate Cancer. |
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| Relations |
| BioSample |
SAMN08929691 |
| SRA |
SRX3933406 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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