EXPERIMENT_TITLE: GSM8170400: EndoC-BH1 Hi-C replicate A, technical replicate 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C library preparation on two replicates of Endo-C BH1 cells was performed using the Arima-HiC kit 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 (targeting ^GATC and G^ANTC) 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. The size-selected fragments were then enriched using enrichment beads (provided in the Arima-HiC kit). The resulting fragments were converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2S Plus DNA Library Kit and Swift 2S Indexing Kit. The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System at 2x101 base pairs.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We used ATAC-seq, RNA-seq, and promoter to create atlases of the regulatory elements to provide context to type 2 diabetes associated variants from publically available genome-wide association studies Overall design: We performed ATAC-seq, RNA-seq, and Promoter Capture C/HiC on EndoC-BH1, HepG2, and SGBS cells
SAMPLE_TITLE: EndoC-BH1 Hi-C replicate A, technical replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Islet-like"}, {"TAG": "tissue", "VALUE": "Islet-like"}, {"TAG": "cell line", "VALUE": "EndoC-BH1"}, {"TAG": "cell type", "VALUE": "Pancreatic Beta cell line"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "EndoCBH1_HiC_A_S1_R1_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR28462357/EndoCBH1_HiC_A_S1_R1_001.fastq.gz.1", "size": "119209643227", "date": "2024-03-26 14:31:29", "md5": "905d5bfb00e48cd18ef761dc3a99b1c5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "EndoCBH1_HiC_A_S1_R2_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR28462357/EndoCBH1_HiC_A_S1_R2_001.fastq.gz.1", "size": "124626090858", "date": "2024-03-26 14:38:19", "md5": "e5f6b5f06b3bbe8288a1fb546be005ce", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]