|
| Status |
Public on Sep 11, 2024 |
| Title |
siSTAMBPL1_1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
cell line: Huh7
cell type: HCC
genotype: siSTAMBPL1
treatment: Transfection
|
| Treatment protocol |
siRNA transfected by lipo 2000（Thermofisher）
|
| Growth protocol |
Huh7 cell lines cultured in DMEM with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PacBio single-molecule real-time (SMRT) sequencing was conducted at Grandomics Biosciences Co., Ltd. (Beijing, China) according to standard procedures. Briefly, the full-length cDNA was synthesized from the total RNA using a SMART PCR cDNA Synthesis Kit.
Average 20-kb-insert-size libraries were constructed using an SMRTbell template prep kit 1.0 and then sequenced on a PacBio Sequel instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
PacBio RS |
| |
|
| Data processing |
The low-quality raw data was removed using SMRTlink (minLength = 50, minReadScore = 0.75). The SUPPA2 (https://github.com/comprna/SUPPA) was used to determine differential splicing events and all genes with intron retention events were used for KEGG analysis.
Assembly: hg38
Supplementary files format and content: consensus sequence
Library strategy: Long-read Iso-seq
|
| |
|
| Submission date |
Sep 06, 2024 |
| Last update date |
Sep 11, 2024 |
| Contact name |
hongli zhang |
| E-mail(s) |
hlz13084@gmail.com
|
| Phone |
13269195522
|
| Organization name |
Beijing University of Chemical Technology
|
| Street address |
Beijing University of Chemical Technology
|
| City |
beijing |
| State/province |
beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
| |
|
| Platform ID |
GPL19124 |
| Series (1) |
| GSE276508 |
Pacbio long read Iso-sequencing is performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells（Long-read） |
|
| Relations |
| BioSample |
SAMN43521711 |
| SRA |
SRX25992967 |
