|
| Status |
Public on Jul 14, 2023 |
| Title |
M-MØ macrophage MCTO donor1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocyte-derived M-CSF macrophages
disease state: MCTO
|
| Growth protocol |
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from two healthy donors and one MTO patient 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 bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
BGISEQ-500 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: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample
|
| |
|
| Submission date |
Aug 07, 2020 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Miguel A Vega |
| E-mail(s) |
mavega@cib.csic.es
|
| Organization name |
CIB (CSIC)
|
| Street address |
Ramiro de Maeztu 9
|
| City |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE155883 |
Mutations in MAFB that cause Multicentric Carpo Tarsal Osteolysis (MCTO) affect the transcriptome of M-MØ |
|
| Relations |
| BioSample |
SAMN15760130 |
| SRA |
SRX8910018 |
