EXPERIMENT_TITLE: GSM5677609: Human pancreatic alpha cell replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Dissociated cells were resuspended in 2% FBS/1XDPBS at 5 × 106 cells per ml. Cells were sorted using the FACSAriaII (BD Biosciences) (nozzle size 100 μm, low flow rate, sample injection chamber set at 4 °C) through various gating schemes such that beta cells are HPi1(HICO-4F9)+ HPa3(HIC3-2D12)- HIC1-1C10 (HPx2)- NTPDase3+, alpha cells are HPi1(HICO-4F9)+ HPa3(HIC3-2D12)+ HIC1-1C10 (HPx2)- NTPDase3-, and acinar cells are HPi1(HICO-4F9)- HPa3(HIC3-2D12)- HIC1-1C10 (HPx2)+ NTPDase3- Hi-C library preparation on FACS-sorted pancreatic cells was performed using the Arima-HiC kit (Arima Genomics Inc; cat# A410030), according to the manufacturer's protocols. Briefly, cells were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using AmpureXP beads (Beckman Coulter; cat# A63882). The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2S Plus DNA Library Kit (Swift, 21024) and Swift 2S Indexing Kit (Swift, 26148).  The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification (Roche, KK4824)) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System at 2x101 base pairs. Arima Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To understand the cell-type specific regulatory architectures of diabetes risk, we generated transcriptomic and 3D epigenomic profiles from sorted human pancreatic acinar, alpha, and beta cells using Arima Hi-C. Overall design: We performed Arima Hi-C on FACS-sorted human pancreatic acinar, alpha and beta cells. Two biological replicates pooled from 5 healthy donors were sequenced for each cell type.
SAMPLE_TITLE: Human pancreatic alpha cell replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HPAP consortium https://hpap.pmacs.upenn.edu/"}, {"TAG": "cell type", "VALUE": "Human pancreatic alpha cell"}, {"TAG": "donor id", "VALUE": "HPAP040, HPAP045, HPAP066"}, {"TAG": "disease state", "VALUE": "No HX diabetes"}, {"TAG": "age", "VALUE": "35, 27, 58"}, {"TAG": "restriction enzyme", "VALUE": "DpnII [^GATC] Arima [G^ANTC]"}]
Pool_Member_@attributes_sample_title: Human pancreatic alpha cell replicate 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human pancreatic alpha cell replicate 2
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