title: GSM9570178: Single-nucleus ATAC-seq of Macaca fascicularis pineal gland, rep 1; Macaca fascicularis; ATAC-seq
library_name: GSM9570178
library_construction_protocol: In this experiment, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used to construct the single-nucleus RNA-seq library. The tissue was processed to extract single nuclei, ensuring that the nuclei quality met the standards for downstream snRNA-seq analysis. The extracted nuclei were encapsulated with barcoded gel beads (GEMs) using the 10X Genomics Chromium Single Cell 3' Reagent Kit v3.1, enabling the capture and labeling of poly(A)+ RNA for downstream sequencing. For snATAC-seq, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used as the source material. The tissue was processed to extract high-quality nuclei. Tn5 transposase was used to cleave the DNA in open chromatin regions within the nuclei, inserting sequencing adapters. The transposition products were encapsulated with ATAC reagents in GEMs on a microfluidic chip, allowing for the capture of chromatin accessibility information for subsequent analysis. For spatial transcriptomics, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was prepared using the BMKMANU Spatial Transcriptomics Gene Expression Kit. The tissue was sectioned into 10 μm slices, which were then transferred to a BMKMANU S3000 Gene Expression Slide for further processing. After fixation and H&E staining, permeabilization was performed, followed by imaging to determine the optimal conditions for library construction. For snRNA-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus. For snATAC-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus. For spatial transcriptomics, libraries were constructed following the TruSeq Illumina library preparation method. Illumina adapters were added to the library, followed by PCR amplification. The libraries were quantified using Qubit 4.0. After ensuring the library quality, sequencing was conducted on the Illumina NovaSeq X Plus platform using the PE150 strategy, targeting at least 150,000 read pairs per spatial point.