|
| Status |
Public on May 10, 2024 |
| Title |
THP-1_DMSO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
strain: human acute myeloid leukemia cells
genotype: THP-1 cells treated with DMSO
|
| Treatment protocol |
1 uM Decitabine or DMSO was incubated with THP-1 cells for 48 hours
|
| Growth protocol |
THP-1 cells were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
C1
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: gene expression text file includes raw counts and FPKM values for each Sample
|
| |
|
| Submission date |
Apr 08, 2022 |
| Last update date |
May 10, 2024 |
| Contact name |
hezhou guo |
| E-mail(s) |
344796247@qq.com
|
| Organization name |
Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
|
| Street address |
Shanghai, P. R. China. No. 197 Rui Jin Er Road
|
| City |
shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE200510 |
Decitabine induces the expression of genes in THP-1 cells |
|
| Relations |
| BioSample |
SAMN27480812 |
| SRA |
SRX14788457 |
