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| Status |
Public on Nov 03, 2022 |
| Title |
Normal1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Homo sapiens |
| Characteristics |
cell type: liver hepatocellular carcinoma
tissue: liver
cell line: HepG2
phenotype: wild type
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| Treatment protocol |
none
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| Growth protocol |
HepG2 cells were cultured in DMEM medium containing fetal bovine serum and antibiotics and placed in incubator with 5% carbon dioxide at 37 C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Different groups of HepG2 cell lines were flash frozen on dry ice, and RNA was harvested using Trizol reagent.We used 2 ug total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard nova6000 Illumina PE150 protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Nova6000 software used for basecalling.
After analyzing the RNA integrity of the sample and whether there is DNA contamination, Nanodrop is used to quantify and detect the RNA concentration and purity, and then use the Agilent 2100 bioanalyze to accurately detect the RNA integrity.
After the library is constructed, Qubit 2.0 is used for preliminary quantification, then Agilent 2100 is used to detect the Insert size of the library, and then the effective concentration of the library is accurately quantified using the qRT-PCR method to ensure the quality of the library.
Perform Illumina PE150 sequencing after pooling according to the effective concentration of the library and data output requirements. After the sequencing is completed, it is mainly based on the statistics of sequencing error rate, data volume, comparison rate, etc., to evaluate that the sequencing of the library is up to the standard for subsequent analysis.
Genome_build: mm9
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| Submission date |
Nov 04, 2020 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Luyuan Ma Luyuan Ma |
| E-mail(s) |
miraclexxj@126.com
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| Phone |
86-13623319263
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| Organization name |
the Third Hospital of Hebei Medical University
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| Street address |
No.68, Xiangjiang Road
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| City |
Shijiazhuang |
| ZIP/Postal code |
050000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE160812 |
Different expression of lincRNAs between wild type and oxaliplatin resistant HepG2 cell line |
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| Relations |
| BioSample |
SAMN16661621 |
| SRA |
SRX9430913 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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