NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4711224 Query DataSets for GSM4711224
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
 
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

Supplementary file Size Download File type/resource
GSM4711224_MSF20_readcount.txt.gz 193.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap