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| Status |
Public on Dec 10, 2018 |
| Title |
DPN 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Hepatocellular Carcinoma
cell line: HepG2
treatment: DPN
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| Treatment protocol |
1 × 10^5 /ml cells were seeded, and when 70%-80% confluent, medium was starved in 0.1% FBS 16 hours before treatment. DMSO, 17β E2 PPT, DPN (1 microM) treat for 48 hours.
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| Growth protocol |
HepG2 cells from American Type Culture Collection, maintained in phenol red-free DMEM supplemented with heat-inactivated and charcoal-stripped FBS and antibiotics.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using RNeasy Mini Kit (Qiagen, Foster City, CA, USA)
Libraries were sequenced as single-end 50 bp on Illumina NextSeq2000 sequencing system at University of Cincinnati. Approximately 27-30 millions of reads were retrieved from each sample
Automated, strand-specific library preparation method using PrepX RNA-Seq samples and a library preparation kit (WaferGen Biosystems, Fremont, CA, USA) with Apollo 324 NGS automated library prep system (WaferGen Biosystems)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Single-end sequencing reads were aligned to the human genome (ENSEMBL GRCh38.p10) using using standard Illumina sequence analysis pipeline
Differential gene expression analysis was performed by DESeq2
Expression data were normalized with DESeq2
differentially expressed genes (|log2 fold change| > 1.5; Padj < 0.01)
Genome_build: gene transcripts were mapped to human genome (ENSEMBL GRCh38.p10)
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| Submission date |
Apr 11, 2018 |
| Last update date |
Dec 10, 2018 |
| Contact name |
Haifei Shi |
| E-mail(s) |
shih@miamioh.edu
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| Phone |
5135293162
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| Organization name |
Miami University
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| Department |
Biology
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| Street address |
700 E High Street
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| City |
Oxford |
| State/province |
OH |
| ZIP/Postal code |
45056 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE112983 |
RNA sequencing of HepG2 cells treated with estradiol or estrogen receptor agonist |
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| Relations |
| BioSample |
SAMN08915752 |
| SRA |
SRX3923769 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3092645_raw_read_counts_DPN_1.xlsx |
384.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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