|
| Status |
Public on Aug 09, 2021 |
| Title |
M2 134 24H |
| Sample type |
SRA |
| |
|
| Source name |
M2 macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocyte-derived M-CSF macrophages
|
| Growth protocol |
For in vitro generation of M2 macrophages, monocytes were incubated with 10 ng/mL M-CSF for 7 days renewing cytokines every 3 days.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal calf serum (FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin RNA purification kit from Macherey-Nagel
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
K2
|
| Data processing |
DNBseq platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene ID and FPKM values for each sample
|
| |
|
| Submission date |
Mar 31, 2021 |
| Last update date |
Aug 09, 2021 |
| Contact name |
Rafael Samaniego |
| E-mail(s) |
inmunooncolab@gmail.com
|
| Organization name |
Fundación para la Investigación Biomédica del Hospital Gregorio Marañón
|
| Lab |
Inmunooncología
|
| Street address |
Calle Dr Esquerdo 46
|
| City |
Madrid |
| ZIP/Postal code |
28007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE171277 |
Characterization of tumor associated macrophages (TAM) in the tumor microenvironment of human melanoma |
|
| Relations |
| BioSample |
SAMN18578333 |
| SRA |
SRX10492200 |
