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| Status |
Public on Aug 03, 2015 |
| Title |
SI_8029-1-8.2-dht-polya |
| Sample type |
SRA |
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| Source name |
VcaP_DHT_polyA selection
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| Organism |
Homo sapiens |
| Characteristics |
cell ;ome: VcaP
cell type: Immortalized prostate cancer cell line
treated with: DHT (dihydrotestosterone)
time point: 24 hrs post-treatment
library preparation protocol: poly(A)+ selection
rin: 8.2
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| Treatment protocol |
After 24 hours, cells were treated either with androgen (1nM 5α-dihydrotestosterone, DHT) or anti-androgen (enzalutamide, MDV3100, MDV). Cells were harvested for RNA isolation at 24 hours post-treatment.
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| Growth protocol |
Immortalized prostate cancer VCaP cell line was obtained from the American Type Culture Collection (Manassas, VA) and was grown in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin. Before the treatments cells were grown in androgen-depleted media lacking phenol red and supplemented with 10% charcoal-stripped serum and 1% penicillin-streptomycin.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Qiagen AllPrep Kit (cat. no. 80404)
Details of the capture RNA-seq and poly(A) RNA-seq library preparation protocols are provided as Supplementary Data. Briefly, for capture libraries we start with 1-3µg of total RNA, and proceed through first-strand synthesis, second strand synthesis, end repair, A-tailing, adapter ligation, size selection on 3% agarose gel, uridine digestion, hybridization to capture probes, washing, and a final PCR step. For poly(A) libraries the protocol is the same, but the last capture and PCR step is omitted and replaced with oligo dT bead selection on input RNA. The stranded capture and poly(A) libraries were sequenced on an Illumina HiSeq 2500 using V3 chemistry.
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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 |
File were aligned using STAR v 3
Reads were counted within Ensembl 75 exon regions that intersect Agilent Whome-Exome Capture V4 probes. FeatureCounts in paired-end mode excluding multi-mapped reads but including duplicate reads was used in stranded mode.
Genome_build: GRCh37
Supplementary_files_format_and_content: featureCounts file format
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| Submission date |
Dec 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Marcin Piotr Cieslik |
| E-mail(s) |
marcin.cieslik@gmail.com
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| Organization name |
University of Michigan
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| Department |
Pathology
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| Lab |
MCTP
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| Street address |
500 S State St
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| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48104 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE64113 |
Comparison of poly(A) and capture RNA-seq: controlled degradation in vitro |
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| Relations |
| BioSample |
SAMN03263794 |
| SRA |
SRX807247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1564670_SI_8029_C4D5HACXX_nsort_featc_agi-cts.cts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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