title: Single Cell ATAC-seq of mus musculus embryonic tissue
design: The scATAC-seq libraries were generated in accordance with the recommended protocol provided by 10x Genomics (Chromium Single Cell ATAC). In summary, 5l of resuspended nuclei dilution was combined with 10l of Transposition Mix to yield a final volume of 15l. These samples were then subjected to an incubation step in a thermal cycler at 37C for 30 minutes. GEM Generation was generated using the Chromium Next GEM Chip H, following the protocol of the manufacturer. After the incubation, 40l of eluted DNA was retrieved using the magnetic separator. An additional cleanup step was conducted using reagent SPRIselect (Beckman Coulter SPRIselect Reagent Kit B23318). For library preparation, each sample was supplemented with 57.5l of Sample Index PCR Mix along with 2.5l of individual Single Index N Set A (3000427). These samples were then incubated following the 10x Genomics protocol (Step 4.1 Sample Index PCR) for a specified number of cycles that match the targeted nuclei recovery. Subsequent to amplification, fragment size selection was carried out using SPRIselect (Step 4.2 Post Sample Index Double Sided Size Selection) until a recovered sample volume of 20l was obtained. DNA quantification using Qubit was performed for each sample. Chicken HH22 library contained 6.5 ng/l and mouse E11.5 library contained 4 ng/l. The resulting libraries were stored at -20C until sequencing. Libraries were sequenced using the Illumina NGS HiSeq3000 available at the Institute of Clinical Molecular Biology (IKMB, Christian Albrechts University in Kiel, Germany), using Illumina kitPE50, targeting sequencing depth of 50k reads per nucleus.
identifiers.namespace: SUB14694584
identifiers.id: E10_FEZ_ATAC