|
| Status |
Public on Jan 30, 2019 |
| Title |
macrophages_donor2_butyrate |
| Sample type |
SRA |
| |
|
| Source name |
Monocyte-derived macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Monocyte-derived macrophages
donor: Donor 2
condition: Butyrate
|
| Treatment protocol |
After 2 washes with PBS, adherent monocytes were differentiated into Mϕ over the period of 5 days in presence of 100 ng/ml M-CSF in RPMI supplemented with 10% fetal calf serum (FCS) (Sigma-Aldrich), 100 U/ml penicillin, 100 μg/ml streptomycin, 30 mM HEPES, and 0.05 mM β-mercaptoethanol.
|
| Growth protocol |
Peripheral blood mononuclear cells (PBMC) were obtained by ficoll gradient. Monocyte-derived macrophages were generated using adherence method selection and M-CSF differentiation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA-sequencing libraries were generated using the 10x Genomics Single Cell 3’ Solution (version 2) and subjected to Illumina sequencing (HiSeq 4000)
10x Genomics Chromium™ Single Cell 3' Reagent Kit (v2 Chemistry)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Single cells from donor 2 butyrate condition.
|
| Data processing |
Reads were aligned using 10x Genomics Cell Ranger pipeline (version 2.0.2) and human reference sequences (version 1.2.0).
To circumvent known index-hopping issues with the HiSeq 4000 platform, cell barcodes common to more than one sample were removed from the aggregated count matrix.
UMI counts were randomly down-sampled so as to normalize the median number of per-cell counts between the samples.
Cells with > 20% mitochondrial reads or fewer than 500 genes were excluded from the analysis.
Genome_build: GRCh38-1.2.0
|
| |
|
| Submission date |
Feb 23, 2018 |
| Last update date |
Jan 30, 2019 |
| Contact name |
Fiona Powrie |
| E-mail(s) |
fiona.powrie@kennedy.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences
|
| Lab |
Kennedy Institute of Rheumatology
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7FY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE111049 |
The commensal-derived metabolite butyrate imprints an antimicrobial program in macrophages |
|
| Relations |
| BioSample |
SAMN08585429 |
| SRA |
SRX3738229 |
