EXPERIMENT_TITLE: GSM6617904: LALB-HIC-Pro-Cap; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Promoter-Capture HiC : Cells were crosslinked with 1% formaldheyde, digested with a restriction enzyme cocktail, end-labeled with Biotin-14-dATP and then followed by ligation. The ligated chromatin was reverse cross-linked and sonicated using Bioruptor ultrasonicator to produce 300-500 bp fragments. Fragmented DNA was then size-selected to have a size distribution between 200-600 bp, and finally subjected to biotin enrichment Promoter-Caputre HiC : DNA libraries were prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Bioscences, Cat. No. 21024), and the resulting libraries were amplified using the KAPA library amplification kit. Subsequently libraries were hybridized to specific SureSelect XT Human capture libraries (Agilent Technologies) and sequenced in paired-end mode (2×75 bp) with NextSeq 500 (Illumina, CA).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Numerous evidence report that non-genetic-driven events such as enhancer reprogramming promotes neoplastic transformation and strongly contribute to the phenotypical  heterogeneity of cancers as much as genetic variation. In this study, we investigated the role of enhancers in sustaining oncogenic transformation in Paediatric B-cell Acute Lymphoblastic Leukemia (ALL-B), a type of cancer caused by the accumulation of lymphoid progenitor cells in the bone marrow. Overall design: Analysis of ATACseq and RNAseq across the type-B acute lymphoblasitc leukemia cancer progression. Four cancer stages are considered: Healthy, Onset, Remission and Relapse scMultiomics samples profiled through 10xGenomics
SAMPLE_TITLE: LALB-HIC-Pro-Cap
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Bone Marrow"}, {"TAG": "tissue", "VALUE": "Bone Marrow"}, {"TAG": "disease state", "VALUE": "Pediatric B-cell acute lymphoblastic leukemia"}, {"TAG": "cell type", "VALUE": "Primary B-cell CD138+"}, {"TAG": "cell line", "VALUE": "LAL-B"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: LALB-HIC-Pro-Cap
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LALB-HIC-Pro-Cap
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "IRE-LalB-siCTR-001-HIC-Pro-Cap-15-10-20_R1.fastq.gz", "size": "10987964994", "date": "2022-10-06 14:01:44", "md5": "e5f9d3002afec8eb0bd96d5eef78ece9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "IRE-LalB-siCTR-001-HIC-Pro-Cap-15-10-20_R2.fastq.gz", "size": "11146138927", "date": "2022-10-06 14:03:37", "md5": "06a1ba084422208c641dda1a15c4ca03", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR21824294", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21824294/SRR21824294", "size": "13665079300", "date": "2022-10-06 14:07:36", "md5": "fa090383eb7b927b4a2798b6c17a805d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR21824294.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR021/21824/SRR21824294/SRR21824294.lite.1", "size": "8737156560", "date": "2022-10-14 02:31:30", "md5": "27911be0e90881904a09fa9beddc05b0", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]