|
| Status |
Public on Aug 21, 2022 |
| Title |
THP-1 macrophages DFO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: wild type
treatment: deferoxamine
|
| Treatment protocol |
THP-1 macrophages were pretreated with 100 μM FAC or 100 μM DFO for 8 h, followed by treatment with F. nucleatum at a multiplicity of infection (MOI) of 10 for 3 h.
|
| Growth protocol |
THP-1 monocytes were differentiated into macrophages using 6 ng/mL phorbol 12-myristate 13-acetate for 48 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from THP1 cells using TRIzol reagent. TruSeq Stranded mRNA Library Prep kit (#RS-122-2101; Illumina) was used with 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 NextSeq 500 |
| |
|
| Data processing |
NextSeq Control Software v4 were used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using Trim Galore, then mapped to hg38 whole genome using HISTAT2.
Differential expression analysis was performed using the DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files for differential gene expression between FAC-treated macrophages relative to DFO-treated macrophages.
|
| |
|
| Submission date |
Dec 21, 2021 |
| Last update date |
Aug 21, 2022 |
| Contact name |
Taishi Yamane |
| E-mail(s) |
[email protected]
|
| Organization name |
1. Department of Cell Signaling and Metabolic Medicine, Faculty of Life Sciences, Kumamoto University
|
| Street address |
1-1-1 Honjo
|
| City |
Kumamoto |
| ZIP/Postal code |
860-8556 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE192400 |
Gene expression of THP-1 macrophages co-cultured with F. nucleatum under iron-deficient and iron-overload conditions |
|
| Relations |
| BioSample |
SAMN24286923 |
| SRA |
SRX13474950 |
