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| Status |
Public on Feb 07, 2019 |
| Title |
L_T0_rep1 |
| Sample type |
SRA |
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| Source name |
LNCaP
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| Organism |
Homo sapiens |
| Characteristics |
days post-selection: 0
cell line: LNCaP
cell type: prostate cancer cell line
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| Treatment protocol |
Cell lines were infected with the library at an MOI of ~ 0.3 such that every shRNA was represented in 300 cells. 24 hrs after infection, cells were selected with puromycin for 48-72 hrs (PC-3, 3.5 µg/mL, 22Rv1, V16A, 3 µg/mL, LNCaP, 2.5 µg/mL). Following selection, cells were split into triplicates, passaged every 3-4 days, and maintained at 300x coverage for the duration of the screen. Cells were sampled in replicates on Day 0, Day 8 and Day 16 post- selection for genomic DNA analysis.
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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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted for replicate samples (QIAamp Blood Midi kit)
shRNA inserts were amplified by PCR using standard Illumina library sequencing. 250x genomic DNA was used as input for each sample and resulting libraries were sequenced on an Illumina HiSeq2500.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 7
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| Data processing |
Sequencing FASTQ files were first trimmed so that shRNA sequence starts at the first base.
Essential circRNAs were identified from shRNA screen sequencing results with MAGeCK (v0.5.4) software
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for shRNA count
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| Submission date |
Apr 13, 2018 |
| Last update date |
Feb 07, 2019 |
| 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) |
| GSE113119 |
Loss of function shRNA screen on circRNA and linear genes in PCa cell lines |
| GSE113124 |
Widespread and Functional RNA Circularization in Localized Prostate Cancer. |
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| Relations |
| BioSample |
SAMN08929909 |
| SRA |
SRX3933613 |
| 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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