Journal: Nature

Article Title: Spatial profiling of chromatin accessibility in mouse and human tissues

doi: 10.1038/s41586-022-05094-1

Figure Lengend Snippet: A tissue section on a standard aminated glass slide was lightly fixed with formaldehyde. Then, Tn5 transposition was performed at 37 °C, and the adapters containing ligation linker 1 were inserted to the cleaved genomic DNA at transposase accessible sites. Afterwards, a set of DNA barcode A solutions were introduced by microchannel-guided flow delivery to perform in situ ligation reaction for appending a distinct spatial barcode Ai (i = 1–50) and ligation linker 2. Then, a second set of barcodes Bj (j = 1-50) were introduced using another set of microfluidic channels perpendicularly to those in the first flow barcoding step, which were subsequently ligated at the intersections, resulting in a mosaic of tissue pixels, each containing a distinct combination of barcodes Ai and Bj (i = 1–50, j = 1–50). After DNA fragments were collected by reversing cross-linking, the library construction was completed during PCR amplification.

Article Snippet: For library construction, the lysate was first purified using the Zymo DNA Clean & Concentrator-5 kit and eluted into 20 μl of DNA elution buffer, followed by mixing with the PCR solution (2.5 µl 25 µM new P5 PCR primer, 2.5 µl 25 µM Ad2 primer, 25 µl 2× NEBNext Master Mix).

Techniques: Ligation, In Situ, Amplification