|
| Status |
Public on Oct 23, 2018 |
| Title |
Control shRNA |
| Sample type |
SRA |
| |
|
| Source name |
PC-3 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tag: PC-3
transfection: Perform sequence after transfection with Control shRNA for 7 days
cell type: Prostate cancer cell
gentoype: KMT2D normal
|
| Treatment protocol |
PC-3 cells (3×105/well) were seeded in 6-well plates and transfected with shRNA expressing lentivirus for 1 week
|
| Growth protocol |
Human prostate cancer cells PC-3 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for RNA sequencing (RNA-seq) was isolated from PC-3 cells transfected with shRNA expressing lentivirus for 1 week. After extracting from cells, total RNA was quantified and integrity measured by BioAnalyzer 2100. Oligo (dT) magnetic beads were used to select mRNA with polyA tail and the target RNA was obtained after purification.
Fragmented the target RNA and reversed transcription to double-strand cDNA (dscDNA) by N6 random primer. Then End repair was performed. The dscDNA was ligated with adaptor and amplified by PCR. Denatured the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
BGISEQ-500
|
| Data processing |
Data Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads
Reads Mapping performed by Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
Gene quantified by FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Feb 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shidong Lv |
| E-mail(s) |
lsd990@163.com
|
| Phone |
02061641114
|
| Organization name |
Nanfang Hospital
|
| Street address |
1838 Guangzhou North Ave.
|
| City |
Guangzhou |
| State/province |
State... |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE94807 |
Next Generation Sequencing Facilitates Quantitative Analysis of KMT2D Knockdown/Control PC-3 Cell Line Transcriptomes |
| GSE94817 |
Analysis of KMT2D Knockdown/Control PC-3 Cell Line |
|
| Relations |
| BioSample |
SAMN06324070 |
| SRA |
SRX2600790 |
