|
Status |
Public on May 15, 2024 |
Title |
group1,Atosiban1_2 |
Sample type |
SRA |
|
|
Source name |
Liver cancer
|
Organism |
Homo sapiens |
Characteristics |
tissue: Liver cancer cell line: organoid cell type: human organoids group: group1,Atosiban1
|
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.
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|
|
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 |
SAMN41133121 |
SRA |
SRX24406823 |