NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1692629 Query DataSets for GSM1692629
Status Public on Feb 25, 2016
Title MAC_RNASeq_Rep1
Sample type SRA
 
Source name Macrophages
Organism Mus musculus
Characteristics strain: 129
cell type: ES derived Macrophages (CD11b+)
Growth protocol A mouse ES cell line carrying a brachyury GFP+ reporter gene (Fehling et al, 2003, Development 130, 4217-4227) was cultured on MEFs then differentiated as described previously (Sroczynska et al, 2009, Methods Mol Biol 538, 317-334.). Both GFP and cell surface markers were used to isolate each cell population. After differentiation of ESC into embryoid bodies, mesodermal cells were isolated by FACs sorting GFP/Brachyury (Bry+, Flk1- negative cells. A proportion of these cells were allowed to differentiate towards hemangioblasts (HBs, Bry+/Flk1+), hemogenic endothelium (HEs, Tie2+/cKit+/CD41-) and haematopoietic progenitors (HPs, CD41+). Macrophages were isolated by terminal differentiation of CD41+ cells to those expressing the macrophage marker CD11b.
Extracted molecule total RNA
Extraction protocol RNA was isolated from snap frozen cells with the RNeasy Plus Mini Kit (Qiagen) and ribosome depleted with the Ribozero Gold Kit (Epicentre) according to manufacturers instructions.
RNA-seq libraries were generated with the SOLiD Total RNA-Seq Kit (Life Technologies, 4445374).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Data processing The sequence reads were mapped to the mm10 mouse genome build using SHRiMP.
The resulting alignment files were used to obtain the transcript abundances as RPKM using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: csfasta and qual files (unmapped reads) and normalised expression as RPKM in a tab delimited file as calculated from Cufflinks
 
Submission date May 20, 2015
Last update date May 15, 2019
Contact name MS Vijayabaskar
E-mail(s) fbsvbm@leeds.ac.uk
Organization name University of Leeds
Department School of Molecular and Cellular Biology
Street address Woodhouse Lane
City Leeds
ZIP/Postal code LS2 9JT
Country United Kingdom
 
Platform ID GPL15907
Series (2)
GSE69080 Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (RNA-seq)
GSE69101 Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development
Relations
BioSample SAMN03703101
SRA SRX1034535

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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