|
Status |
Public on Dec 09, 2020 |
Title |
siRNA MAF donor #3 |
Sample type |
SRA |
|
|
Source name |
macrophages
|
Organism |
Homo sapiens |
Characteristics |
cell: Monocyte-derived M-CSF macrophages sirna: siMAF
|
Treatment protocol |
Macrophages were transfected with either Control siRNA or MAFB-specific siRNA or MAF-specific siRNA for 24h
|
Growth protocol |
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from 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 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 HISAT2 with default parameters. Read counts for each gene were calculated using htseq-count Genome_build: GRCh38 Supplementary_files_format_and_content: Table with raw gene counts for every gene (denoted as Ensemble gene ID) and every sample
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|
|
Submission date |
Aug 05, 2020 |
Last update date |
Dec 09, 2020 |
Contact name |
Miguel A Vega |
E-mail(s) |
[email protected]
|
Organization name |
CIB (CSIC)
|
Street address |
Ramiro de Maeztu 9
|
City |
Madrid |
ZIP/Postal code |
28040 |
Country |
Spain |
|
|
Platform ID |
GPL23227 |
Series (1) |
GSE155719 |
Transcriptional effects of MAF- and MAFB-siRNAs on M-CSF-derived macrophages |
|
Relations |
BioSample |
SAMN15734524 |
SRA |
SRX8889735 |