EXPERIMENT_TITLE: GSM4989581: CLL_401_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were prepared using the Arima Genomics kit (Arima Genomics, San Diego, CA) in conjunction with the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 21024) and Swift Biosciences Indexing Kit (Cat # 26148) following the manufacturer's recommendations. In brief, 1X 106 cells were fixed with formaldehyde in the nucleus. Fixed cells were permeabilized using a lysis buffer and then digested with a restriction enzyme cocktail supplied in the Arima HiC kit. The resulting overhangs were filled in with biotinylated nucleotides followed by ligation. After ligation, crosslinks were reversed, and the DNA was purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. Hi-C material was then sonicated using a Covaris Focused-Ultrasonicator M220 instrument to achieve 300-500 bp fragment sizes. The sonicated DNA was double-size selected using Ampure XP beads. Hi-C sequencing libraries were generated using low input Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 21024) and Swift Biosciences Indexing Kit (Cat # 26148). The Hi-C libraries were loaded on an Illumina flow cell for paired-end 150-nucleotide read length sequencing on the Illumina HiSeq 4000 following the manufacturer's protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. Various computational methods have been developed to predict chromatin interactions. Most of these methods rely on large collections of ChIP-Seq/RNA-Seq/DNase-Seq datasets and predict only enhancer-promoter interactions. Some of the 'state-of-the-art' methods have poor experimental designs, leading to over-exaggerated performances and misleading conclusions. Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin regions by using only DNA sequences of the interacting open chromatin regions. CHINN is able to predict CTCF-, RNA polymerase II- and HiC-associated chromatin interactions between open chromatin regions. CHINN also shows good across-sample performances and captures various sequence features that are predictive of chromatin interactions. We applied CHINN to 90 chronic lymphocytic leukemia (CLL) samples and detected systematic differences in the chromatin interactome between IGVH-mutated and IGVH-unmutated CLL samples. Overall design: We generated Hi-C, ATAC-seq, and RNA-seq libraries for 6 CLL samples. Chronic Lymphocytic Leukemia patient samples (either peripheral blood or bone marrow isolates) were obtained from the Leukemia Cell Bank at the National University Health System (NUHS) with patient consent, under Institute Review Board number H-20-022E. The CLL samples were either bone marrow aspirates (312,324,344,484, and 102) or peripheral blood (401).
SAMPLE_TITLE: CLL_401_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "CLL 401 cells"}, {"TAG": "disease state", "VALUE": "Chronic Lymphocytic Leukemia"}, {"TAG": "tissue", "VALUE": "peripheral blood"}, {"TAG": "cell type", "VALUE": "CLL 401 cells"}]
Pool_Member_@attributes_sample_title: CLL_401_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: CLL_401_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SA_AD401_DKDL192000465-1a_H5MKVBBXX_L4_1.fq.gz", "size": "45790349189", "date": "2020-12-29 16:23:43", "md5": "1642dc7a259b59b8367ea048b0c9550f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SA_AD401_DKDL192000465-1a_H5MKVBBXX_L4_2.fq.gz", "size": "45360939692", "date": "2020-12-29 15:28:38", "md5": "5c209c1721d0a63586c73eb736863c0e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13310976", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13310976/SRR13310976", "size": "60920657593", "date": "2020-12-29 20:16:43", "md5": "9ca2a2c766682ee34302749c6f41952d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13310976.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR013/13310/SRR13310976/SRR13310976.lite.1", "size": "34849743753", "date": "2022-08-10 02:29:45", "md5": "a73cc34b9e327cd15a80c531a3b43d25", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]