|
| Status |
Public on May 26, 2021 |
| Title |
MF_5 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: macrophages derived from CD14+ monocytes
treatment: untreated
|
| Treatment protocol |
Human macrophages were stimulated with apoptotic Jurkat cells at a 1:3 ratio in 6-well plates for 3 hours. Upon efferocytosis, non-phagocytosed cells were removed and macrophages were washed 3x with PBS, followed by incubation with RPMI 1640 supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin for 3 hours.
|
| Growth protocol |
CD14+ monocytes isolated from human buffy coats and differentiated into macrophages in macrophage serum-free medium supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 50 ng/mL of macrophage colony-stimulating factor (M-CSF) for 7 days followed by culture in RPMI 1640 medium supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of non-treated and efferocytotic macrophages was isolated using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Normalized_counts_MF
|
| Data processing |
raw data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
[Trimming] bbduk v35.92
[Alignment] STAR Aligner with modified ENCODE settings
[Gene Read Counting] HTSeq-count with kit-specic options (FWD)
[Differential Analysis] DESeq2 Pipeline
Genome_build: Homo sapiens (GRCh38)
Supplementary_files_format_and_content: text files containing the normalized read counts for MF and MF+AC
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
May 26, 2021 |
| Contact name |
Tobias Schmid |
| Organization name |
Goethe-University Frankfurt
|
| Department |
Institute of Biochemistry I
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE169160 |
Lysosome-dependent LXR and PPARdelta Activation upon Efferocytosis in Human Macrophages |
|
| Relations |
| BioSample |
SAMN18350274 |
| SRA |
SRX10375433 |
