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| Status |
Public on Feb 25, 2016 |
| Title |
MAC_RNASeq_Rep2 |
| Sample type |
SRA |
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| Source name |
Macrophages
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| Organism |
Mus musculus |
| Characteristics |
strain: 129
cell type: ES derived Macrophages (CD11b+)
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| 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
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| Submission date |
May 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
MS Vijayabaskar |
| E-mail(s) |
fbsvbm@leeds.ac.uk
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| Organization name |
University of Leeds
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| Department |
School of Molecular and Cellular Biology
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| Street address |
Woodhouse Lane
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| City |
Leeds |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| BioSample |
SAMN03703102 |
| SRA |
SRX1034536 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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