|
| Status |
Public on Mar 07, 2018 |
| Title |
siNT_E_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1_siNT_E
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 22Rv1
cell type: prostate cancer cells
transfected with: non-target siRNA (designated as ARFL+/ARVs+)
|
| Treatment protocol |
22Rv1 cell were transfected with non-target siRNA (designated as ARFL+/ARVs+) or siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-), then cultured with charcoal-stripped serum (CSS) medium for 72 hours.
|
| Growth protocol |
Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Ribo-zero rRNA remove Kit was used to remove ribosomal RNAs were removed. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include "chrom", "st", "end"," mRNA_size"," strand"," fragment count"," FPM" and "FPKM" values for each Sample.
|
| |
|
| Submission date |
Apr 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
iamyezhenqing@gmail.com
|
| Organization name |
UT Health San Antonio
|
| Department |
6Department of Population Health Sciences
|
| Street address |
8403 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE80741 |
Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [RNA-seq] |
| GSE80743 |
Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression |
|
| Relations |
| BioSample |
SAMN04910119 |
| SRA |
SRX1734371 |
