BioProject

The phosphatidylserine receptor, TIM4, encoded by TIMD4, mediates the phagocytic uptake of apoptotic cells. More...

The phosphatidylserine receptor, TIM4, encoded by TIMD4, mediates the phagocytic uptake of apoptotic cells. To dissect the function of TIM4 in chicken (Gallus gallus), we applied anti-chicken TIM4 monoclonal antibodies in combination with CSF1R reporter transgenes so as to isolate specific cell populations.This dataset comprises RNA-sequencing of blood leukocytes (4 samples) and isolated cells from the liver and bursa (6 samples each) of 4-13 week old CSF1R-mApple transgenic chickens, as purified from different populations based on their expression of TIM4, the CSF1R-mApple reporter transgene or Bu-1 (a B cell surface marker). The samples are: TIM4+ mApple+ and TIM4- mApple+ populations from blood leukocytes, TIM4+ mApple-, TIM4+ mApple+ and TIM4- mApple+ populations from non-parenchymal liver cells, and TIM4+ Bu-1-, TIM4+ Bu-1+ and TIM4- Bu-1+ populations from bursal cells.RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England BioLabs), with each sample containing different index primers (NEBNext Multiplex Oligos for Illumina, index primer set 1), and sequenced by Edinburgh Genomics using the Illumina HiSeq 4000 sequencing platform at a depth of > 290 million strand-specific 75bp paired-end reads.These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact david.hume@uq.edu.au to enquire. Less...