|
Status |
Public on Feb 24, 2021 |
Title |
RNA-seq_D1_MDMs_LPS |
Sample type |
SRA |
|
|
Source name |
Human monocyte-derived macrophages
|
Organism |
Homo sapiens |
Characteristics |
cell type: Human monocyte-derived macrophages donor: Donor 1 treatment: LPS-18h
|
Treatment protocol |
Monocytes, MDMs or MDDCs were stimulated with Pam3CSK4 (1 μg/ml), LPS (10 ng/ml), R837 (10 μg/ml) or R848 (10 μg/ml) for 18 hours.
|
Growth protocol |
Human monocytes were cultured in RPMI-1640 medium with 10% FBS, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 100U/ml penicillin, and 100 µg/mL streptomycin. To differentiate monocytes into macrophages or dendritic cells, recombinant human M-CSF (50ng/mL) or recombinant human GM-CSF (100ng/mL) and recombinant human IL-4 (50ng/mL) were used, respectively. The culture medium which contained fresh recombinant human M-CSF or recombinant human GM-CSF and recombinant human IL-4 was replaced every 2 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using TRIzol reagent and RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Illumina bcl2fastq2.17.04 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and mapped to hg19 whole genome using CLC-Bio Genomics Workbench Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC-Bio Genomics Workbench. Genome_build: hg19
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|
|
Submission date |
Mar 20, 2020 |
Last update date |
Feb 24, 2021 |
Contact name |
Edward Wakeland |
Organization name |
UT Southwestern Medical Center
|
Department |
Immunology
|
Street address |
5323 Harry Hines Blvd
|
City |
Dallas |
State/province |
TX |
ZIP/Postal code |
75390-9093 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE147310 |
IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - TLR stimulation) |
GSE147314 |
Chromatin accessibility dictates specific transcriptional response by different cells of the innate immune system |
|
Relations |
BioSample |
SAMN14418559 |
SRA |
SRX7963423 |