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| Status |
Public on Dec 31, 2018 |
| Title |
C42B_SP-2509_3 |
| Sample type |
SRA |
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| Source name |
prostate cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
cell line: prostate cancer cell line C42B
treatment: SP-2509
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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 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.
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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 |
Sample 6
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| Data processing |
Tophat version 2.0.9 for alignment
Cufflinks version 2.1.1 for transcript assembly
Genome_build: hg19
Supplementary_files_format_and_content: Text file with fpkm-like measurement for each UCSC (v. hg19) transcript
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| Submission date |
Jul 02, 2014 |
| 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 |
SAMN02899697 |
| SRA |
SRX643502 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1424425_Sample_RNA130912JA_3.22.13_C42B_2509_1_3.txt.gz |
457.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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