EXPERIMENT_TITLE: GSM7220198: HiC Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND517; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C library preparation was performed using the Arima-HiC kit (Arima Genomics Inc), 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). The size-selected fragments were then enriched using Enrichment Beads (provided in the Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2SPlus 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 using 200 bp reads
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We used ATAC-seq, RNA-seq, and HiC to create atlases of the regulatory elements to provide context to autoimmune disease associated variants from publically available Genome-wide association studies Overall design: We performed ATAC-seq  and HiC on data from 3 donors
SAMPLE_TITLE: HiC Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND517
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "University of Pennsylvania Human Immunology Core (donor collection) /Center for Spatial and Functional Genomics (cell isolation, library construction, and sequencing)"}, {"TAG": "cell type", "VALUE": "CD4_Tcell"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "naiveT_8hr_ND517_S2_R2_001.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR24268570/naiveT_8hr_ND517_S2_R2_001.fastq.gz.1", "size": "266563315726", "date": "2023-04-23 06:08:06", "md5": "0c2e4c9f356091b6b699a951817dd3a3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "naiveT_8hr_ND517_S2_R1_001.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR24268570/naiveT_8hr_ND517_S2_R1_001.fastq.gz.1", "size": "259305403800", "date": "2023-04-23 04:56:38", "md5": "27dcdacabc4045f73809c863a583410b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]