GSM5903073: Hypoxic renal single cell multiome RNA; Mus musculus; RNA-Seq
Mice exposed to 4 hours of CO (0.1%) induced hypoxia. Kidney FACS sorted cells merged from 5 mice. Sorted cells were processed according to 10x Genomics Chromium Single Cell Multiome ATAC+ Gene Expression low cell number protocol according to protocol number CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB used for cell lysis (0.1x lysis buffer and lysed for 7 min) to obtain intact nuclei. Single cell ATAC and RNA-seq libraries were prepared using the Chromium single cell multiome ATAC + gene expression platform (10x Genomics). Nuclei were prepared and counted to ensure quality and concentration. Nuclei were then transposed according to the manufacturer's protocol.  Transposed nuclei suspension was loaded onto Next GEM Chip J targeting 5000 nuclei and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell gene expression libraries, as well as single cell ATAC-seq libraries, were generated according to the manufacturer's protocol using the Chromium Next GEM Single Cell multiome ATAC+ gene expression kit. Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Each library was sequenced separately on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina), targeting 25,000 reads/nuclei for ATAC-seq and a minimum of 20,000 reads/nuclei for gene expression.