|
| Status |
Public on Apr 01, 2022 |
| Title |
PC3-shHOXB13-2 |
| Sample type |
SRA |
| |
|
| Source name |
prostate tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
treatment/infection: shHOXB13
genotype: WT
|
| Treatment protocol |
LNCaP or PC3 cells were infected with control shRNA (pGIPZ) or shRNA targeting HOXB13 (shHOXB13) lentiviruses for 7 days. LNCaP cells with HOXB13 knockdown were rescued by HOXB13-WT or G84E . LNCaP cells were co-infected with shRNA virus targeting HDAC1 (shHDAC1) and HDAC3 (shHDAC3) with or without concomittant HOXB13 overexpression for 7 days.
|
| Growth protocol |
LNCaP and PC3 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603).using the Illumina provided protocol.
RNA-Seq samples were sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mr272
|
| Data processing |
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of RPKM/FPKM values for each Sample
|
| |
|
| Submission date |
Jun 30, 2020 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
|
| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE153585 |
HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming [RNA-Seq] |
| GSE153586 |
HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming |
|
| Relations |
| BioSample |
SAMN15408409 |
| SRA |
SRX8643186 |
