GSM5141278: ex cDC1 rep2 (RNA-seq); Mus musculus; RNA-Seq
RNA-seq: Cells were FACS sorted based on the following surface parameters. Common pre-gate to all samples: Live, Singlets, CD11c+ Lin- (CD19, TCRb, B220, NK1.1). cDC1_migratory_XCR1Cre+_IRF4_flox (MHC-II high GFP+ XCR1+ CD11b-); cDC1_migratory_XCR1Cre-_IRF4_flox (MHC-II high XCR1+ CD11b-); cDC1_resident_XCR1Cre+_IRF4_flox (MHC-II low GFP+ XCR1+ CD11b-); cDC1_resident_XCR1Cre-_IRF4_flox (MHC-II low XCR1+ CD11b-); cDC1_wt (MHC-II hi YFP+); cDC2_wt (MHC-II hi YFP- CD11b+); ex_cDC1 (MHC-II hi YFP+); cDC2_flox (MHC-II hi YFP- CD11b+); DKO ( MHC-II hi YFP+); RNeasy Micro Kit  according to manufacturers protocol (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer with the RNA 6000 nano kit (Agilent).   ATAC-seq: Briefly, sorted cells (same populations as in RNA-seq: cDC1, cDC2_wt, ex_cDC1 and cDC2_flox) were rinsed with resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water), lysed and immediately after added tagmentation reaction mix from the Nextera DNA library preparation kit (Illumina). After 30  min incubation at 37C, samples were cleaned up using MinElute PCR purification kit (Qiagen). The libraries were constructed and barcoded using a Nextera library preparation kit (Illumina). The final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio for ~100-150bp cutoff DNA size) using SPRI select (Beckman-Coulter). Each biological sample was run in triplicates. Libraries were sequenced paired-end on HiSeq2500 (Illumina) using 50 cycles paired-end mode (Illumina). RNA-seq: RNA was extracted with RNeasy Micro kit (Qiagen). Revere transcription and amplification was performed using Ovation RNA-Seq System V2 kit (NuGEN). Amplified cDNA was purified using the MinElute Reaction Cleanup kit (Qiagen). Final librariers were constructed and indexed with the Ovation Ultralow system V2 kit (NuGEN) and quantified by Agilent 2100 Bioanalyzer (High sensitivity DNA kit).    ATAC-seq:  ATAC-seq library preparation was done as described in (Corces et al. 2017) using Transposomes from Nextera DNA library preparation kit (Illumina) and custom primers. Libraries were run paired-end on the Illumina HiSeq2500.