|
| Status |
Public on Mar 27, 2023 |
| Title |
VDRKO, 1,25(OH)2D3,2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH14).
genotype: VDRKO
treatment: 1,25(OH)2D3
|
| Treatment protocol |
Treatment of 1,25(OH)2D3 and/or antagonist post confluent cells on 6-well platefor 8hrs.
|
| Growth protocol |
HCT116 parent and VDRKO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Add 1ml of TRIZOL per well and extract total RNA according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared using SMARTer stranded RNA-Seq kit v2(Clontech) according to the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
V.KO.VDposi.AHnega_V.KO.VDposi.AHnega.2.
|
| Data processing |
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCh38.p13.chromosomes
Supplementary files format and content: Reads on annotated genes were counted using featureCounts (version 1.6.1).
|
| |
|
| Submission date |
Mar 22, 2023 |
| Last update date |
Mar 28, 2023 |
| Contact name |
Yoshiaki Kanemoto |
| E-mail(s) |
ykanemo164@gmail.com
|
| Phone |
0246815522
|
| Organization name |
Jyoban Hospital
|
| Street address |
kaminodai 57, jyobankamiyunagaya-town
|
| City |
Iwaki |
| State/province |
Fukushima |
| ZIP/Postal code |
972-8322 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE227910 |
Treatment of 1,25(OH)2D3 or Antagonist in HCT116 WT and VDRKO cell lines |
|
| Relations |
| BioSample |
SAMN33850078 |
| SRA |
SRX19746624 |
