|
| Status |
Public on May 15, 2024 |
| Title |
group3,Vehicle3_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver cancer
cell line: organoid
cell type: human organoids
group: group3,Vehicle3
|
| Treatment protocol |
First, three different of human organoid samples were constructed, and then each group of samples was treated with Vehicle and 10 μM Atosiban
|
| Growth protocol |
organoids were maintained in humidified atmosphere with 5% CO2 at 37°C with bioGenousTM Hepatocellular Carcinoma Organoid Kit Catalog: K2105-HCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis of organoids with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
|
| |
|
| Submission date |
Apr 30, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
huijie yang |
| E-mail(s) |
huijie.yang@xxmu.edu.cn
|
| Phone |
17525918203
|
| Organization name |
Xinxiang Medical University
|
| Street address |
Hongqi District, Xinxiang City
|
| City |
xinxing |
| ZIP/Postal code |
453003 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE266229 |
Atosiban harness hepatocellular carcinoma progression in human organoid model |
|
| Relations |
| BioSample |
SAMN41133124 |
| SRA |
SRX24406820 |
