|
Status |
Public on May 26, 2021 |
Title |
MF+AC_1 |
Sample type |
SRA |
|
|
Source name |
peripheral blood
|
Organism |
Homo sapiens |
Characteristics |
cell type: macrophages derived from CD14+ monocytes treatment: co-cultured with apoptotic Jurkat T cells
|
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_reads_MF_AC
|
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 |
SAMN18350272 |
SRA |
SRX10375435 |