|
| Status |
Public on Oct 01, 2022 |
| Title |
LX-2 cells treated with conditioned medium from HCT116Vector cells #2 |
| Sample type |
SRA |
| |
|
| Source name |
LX-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LX-2
cell type: hepatic stellate cells
treatment: cultured for 24h
|
| Growth protocol |
Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Servicebio, Wuhan, China) at a ratio of 106 cells per mL of reagent according to the manufacturer’s instructions.
RNA-sequencing libraries were generated using ribosomal RNA depleted RNAs with the NEBNext Ultra II RNA Library Prep Kit (NEB) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the Bioanalyzer 2100 system (Agilent Technologies, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
1377-LX2-C2
|
| Data processing |
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Minfeng Chen |
| E-mail(s) |
minfengchen@jnu.edu.cn
|
| Phone |
+862085228916
|
| Organization name |
Jinan University
|
| Street address |
Huangpu road 601
|
| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE208084 |
RNA-seq on LX-2 cells treated with conditioned medium from either HCT116Vector or HCT116FGFBP1 cells |
|
| Relations |
| BioSample |
SAMN29680327 |
| SRA |
SRX16174046 |
