GSM6422424: Islet 1384-I F; Mus musculus; ATAC-seq
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204). Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.