|
| Status |
Public on Jun 20, 2019 |
| Title |
RNA-seq_LPS-IFNG-3 |
| Sample type |
SRA |
| |
|
| Source name |
CD14+ Monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD14+ Monocytes
cultured in: M-CSF
treatment: LPS-16h-IFNG-3h
donor: Donor3
|
| Treatment protocol |
CD14+ cells cultured in M-CSF (20ng/ml) were treated with or without LPS (0.1 ng/ml) overnight and then stimulated with IFN-γ (100 U/ml) for 3 hours and cells cultured in GM-CSF (20 ng/ml) were treated with or without IFN-γ (100 U/ml) for 48 hours and then stimulated with LPS (10 ng/ml) for 3 hours
|
| Growth protocol |
Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep kit(E7765L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA seq CD14+ Monocytes
|
| Data processing |
Sequenced reads were mapped to reference human genome (hg38 assembly) using STAR aligner (2.5.3, Dobin et al., 2013 Bioinformatics) with the following parameters: STAR --runThreadN 8 --genomeDir STARIndex --readFilesIn ${j}_R1_001.fastq.gz --readFilesCommand zcat --outFileNamePrefix rnaseq_STAR/${j}.STAR --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --sjdbGTFfile GRCh38_gencode_release29/annotation/genes.gtf --quantMode GeneCounts. The count file matrix was fed into SARTools 1.3.0 DESeq2 or HSS RNA-seq visualization platform (1.3.1) package to obtain differentially gene expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: Tab limited raw HT-seq counts
|
| |
|
| Submission date |
May 01, 2019 |
| Last update date |
Jun 20, 2019 |
| Contact name |
Mahesh Bachu |
| E-mail(s) |
bmahesh07@gmail.com, bachum@hss.edu
|
| Organization name |
Hospital For Special Surgery
|
| Street address |
535 E 70th St 6th Floor
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE120945 |
IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization |
| GSE130567 |
IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [RNA-seq II] |
|
| Relations |
| BioSample |
SAMN11552432 |
| SRA |
SRX5774995 |
