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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2018 |
| Title |
LNCap_DMSO_24h_2 |
| Sample type |
SRA |
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| Source name |
Cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
cell type: prostate cancer cell line LNCap
treatment: DMSO
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| Treatment protocol |
C42B cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment. PC3 cells were treated with 2uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment. LNCaP cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested at 24 and 72hrs post-treatment.
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| Growth protocol |
C42B cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% charcoal-stripped FBS. PC3 cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% FBS. LNCaP cells were plated in triplicate in 6-well plates, 350,000 cells/well in RPMI+10% FBS. LNCaP cells for 24hr treatment conditions were plated in triplicate in 6-well plates, 400,000 cells/well in RPMI+10% FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol+CHCl3
Agilent SureSelect Stranded RNAseq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
0uM SP-2509 24hrs
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| Data processing |
Tophat version 2.0.9 for alignment
Cufflinks version 2.1.1 for transcript assembly
STAR version 2.4.2a for alignment and assembly (LNCaP 24h only)
Genome_build: hg19
Genome_build: GRCh38 (LNCaP 24hr only)
Supplementary_files_format_and_content: Text file with fpkm-like measurement for each UCSC (v. hg19) transcript
Supplementary_files_format_and_content: Tab-delimited STAR output file with raw read counts for each GRCh38 gene (LNCaP 24h only)
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| Submission date |
Jul 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshi Alumkal |
| Organization name |
Knight Cancer Institute
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| Street address |
3303 SW Bond Ave. CH14R
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE59009 |
RNA-seq profiles after SP-2509 Treatment of LNCaP, C42B, and PC3 cells |
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| Relations |
| BioSample |
SAMN05416331 |
| SRA |
SRX1960003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2241881_LNCap_DMSO_24h_2.ReadsPerGene.out.tab.gz |
359.3 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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