|
| Status |
Public on Oct 16, 2024 |
| Title |
Hep3B_C1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
cell line: Hep3B cell line
cell type: Hepatocellular Carcinoma
treatment: shRNA control
|
| Treatment protocol |
PELP1 knockdown (KD) HEP3B cells were generated using human specific PELP1-shRNA1 (TRCN0000159883; Sigma) and PELP1-shRNA2 (TRCN0000159673; Sigma) lentiviral particles. Control cells were created using non-targeted shRNA (SHC016-1EA; Sigma) lentiviral particles. PELP1 knockdown HEP3B cells were selected using puromycin (1mg/ml) selection to produce stable clones, and pooled clones were selected.
|
| Growth protocol |
Hep3B cells were cultured in RPMI medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was isolated using TRIzol reagent (Invitrogen).
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts to obtain the counts per gene
Gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format, which contains geneid, chromosome location (chr, start, end, strand), gene length, and read counts.
|
| |
|
| Submission date |
Feb 01, 2024 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE254860 |
The therapeutic potential and significance of the PELP1 signaling pathway in hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN39735441 |
| SRA |
SRX23503648 |
