|
| Status |
Public on Jun 24, 2015 |
| Title |
PC3_DAXX_KD_1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Prostate cancer
tissue: Prostate
genotype: DAXX knock-down
|
| Growth protocol |
The human prostate cancer cell line PC3 and its DAXX knock-down counterpart were maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine. For the DAXX K/D PC3 cells, the RPMI medium was supplemented with puromycin (Sigma, Cat # P9620; 2 μg/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using NucleoSpin RNA kit (Clontech, cat # 740955). The RNA integrity number (RIN) was determined using The Agilent RNA ScreenTape assay (Agilent 2200 TapeStation, Salk Institute’s Next Generation Sequencing core), and high quality RNA was used for RNA-Seq. The RNA-Seq libraries were prepared using Illumina TruSeq RNA v2 non-stranded sample prep kits and sequenced on an Illumina HiSeq 2500 according to the manufacturer’s instructions.
Illumina HiSeq 2500 system and associated protocol was used. Run type: SE50; Run mode: High Output
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
non-stranded RNA-seq: PC3_DAXX_KD_1
|
| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM
|
| |
|
| Submission date |
May 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
|
| Organization name |
University of California, San Diego (UCSD)
|
| Department |
Medicine
|
| Street address |
9500 Gilman Dr. MC 0640
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE68645 |
The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (RNA-seq) |
| GSE68656 |
The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer |
|
| Relations |
| BioSample |
SAMN03612157 |
| SRA |
SRX1021238 |
