|
| Status |
Public on Aug 11, 2021 |
| Title |
shCtrl_vector_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
transfection: Cells were infected with control shRNAs
|
| Treatment protocol |
LNCaP cell line was established by transducing with lenti-virus containing shControl, shMETTL3 , shMETTL3-resistant METTL3 wildtype and shMETTL3-resistant METTL3 catalytically dead mutant. Cells were selected with 1ug/ml puromycin and cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C.
|
| Growth protocol |
The human prostate adenocarcinoma cell line LNCaP was cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C. All cell lines were routinely tested for mycoplasma contamination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by KAPA Stranded mRNA- Seq Kit (96rxn, KK8421), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample
|
| |
|
| Submission date |
Apr 01, 2020 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Kexin Xu |
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE147884 |
RNA transcriptome analyses in shcontrol, shMETTL3, shMETTL3-resistant METTL3 wildtype and catalytically dead mutant LNCaP cells. |
| GSE147891 |
human prostate cell lines |
|
| Relations |
| BioSample |
SAMN14517538 |
| SRA |
SRX8042009 |
