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| Status |
Public on Aug 11, 2023 |
| Title |
PMB-1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 cells
cell type: hepatocyte
treatment: treated withPMB for 24 hours
tissue: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
cells were collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq was used for differential gene expression analysis
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: Homo_sapiens.GRCh38.89.chr
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Oct 13, 2021 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Yang Gao |
| E-mail(s) |
yxgyang@126.com
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| Phone |
18238837867
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| Organization name |
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College
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| Street address |
Dongcheng District, Tiantan Xili
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| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE185840 |
Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes |
| GSE185844 |
Scavenger Receptor SCARB2 Drives Hepatic Carcinoma Initiation by Enhancing MYC Transcriptional Activity and Supporting Cancer Stem Cell Traits. |
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| Relations |
| BioSample |
SAMN22246872 |
| SRA |
SRX12593084 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5624438_PMB-1.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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