|
| Status |
Public on Feb 24, 2021 |
| Title |
RNA-seq_D1_mono_Pam3CSK4 |
| Sample type |
SRA |
| |
|
| Source name |
Human monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human monocytes
donor: Donor 1
treatment: Pam3CSK4-18h
|
| 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
|
| |
|
| 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 |
SAMN14418582 |
| SRA |
SRX7963373 |
