EXPERIMENT_TITLE: Raw reads: GM12878_CiFi_DpnII
STUDY_DESCRIPTOR_STUDY_ABSTRACT: By coupling chromatin conformation capture (3C) with PacBio HiFi long-read sequencing, we have developed a new method (CiFi) that enables analysis of genome interactions across repetitive genomic regions with low-input requirements. CiFi produces multiple interacting concatemer segments per read, facilitating genome assembly and scaffolding. Together, the approach enables genomic analysis of previously recalcitrant low-complexity loci and of single individuals of tiny organisms, opening new and exciting avenues of research.
SAMPLE_TITLE: GM12878 human lymphoblastoid cell line
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA-FIRST-PUBLIC", "VALUE": "2020-03-06T04:05:11Z"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2020-02-26T23:35:38Z"}, {"TAG": "External Id", "VALUE": "SAMEA6592574"}, {"TAG": "INSDC center name", "VALUE": "UNIVERSITY OF CALIFORNIA - DAVIS"}, {"TAG": "INSDC first public", "VALUE": "2020-03-06T04:05:11Z"}, {"TAG": "INSDC last update", "VALUE": "2020-02-26T23:35:38Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "GM12878"}, {"TAG": "cell type", "VALUE": "Lymphoblastoid cell line"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "sample name", "VALUE": "GM12878"}, {"TAG": "scientific_name", "VALUE": "Homo sapiens"}]
Pool_Member_@attributes_sample_title: GM12878 human lymphoblastoid cell line
RUN_SET_RUN_Pool_Member_@attributes_sample_title: GM12878 human lymphoblastoid cell line
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "XUCMD_20240417_S64411e_PL10194_001_1_A01.hifi_reads.bam", "url": "https://sra-pub-src-2.s3.amazonaws.com/ERR14251239/XUCMD_20240417_S64411e_PL10194_001_1_A01.hifi_reads.bam.1", "size": "20020887858", "date": "2025-02-08 23:07:27", "md5": "3d898839a161768dcbf4582146e497d7", "version": "1", "semantic_name": "bam", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR14251239", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-run-38/ERR014/14251/ERR14251239/ERR14251239.1", "size": "16266715723", "date": "2025-02-08 23:12:49", "md5": "be2153231e63edd0f950a2bdb3c54137", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]