EXPERIMENT_TITLE: HiSeq X Ten paired end sequencing
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: DNAse Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 12% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees.
SAMPLE_TITLE: GM20818 human lymphoblastoid cell line
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA-FIRST-PUBLIC", "VALUE": "2020-03-06T04:05:11Z"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2020-02-26T23:35:54Z"}, {"TAG": "External Id", "VALUE": "SAMEA6592575"}, {"TAG": "INSDC center name", "VALUE": "UNIVERSITY OF CALIFORNIA - DAVIS"}, {"TAG": "INSDC first public", "VALUE": "2020-03-06T04:05:11Z"}, {"TAG": "INSDC last update", "VALUE": "2020-02-26T23:35:54Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "GM20818"}, {"TAG": "cell type", "VALUE": "Lymphoblastoid cell line"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "sample name", "VALUE": "GM20818"}, {"TAG": "scientific_name", "VALUE": "Homo sapiens"}]
Pool_Member_@attributes_sample_title: GM20818 human lymphoblastoid cell line
RUN_SET_RUN_Pool_Member_@attributes_sample_title: GM20818 human lymphoblastoid cell line
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR3966320.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/ERR003/3966/ERR3966320/ERR3966320.lite.1", "size": "8169148831", "date": "2022-08-07 09:39:21", "md5": "b0d2fb92052222a7f9a51c8f05f42fd2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ERR3966320", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR3966320/ERR3966320", "size": "12672965091", "date": "2021-01-01 10:49:37", "md5": "4e554d3c1f1134e3ff428d806f23dc74", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "H20818_2.fq.gz", "size": "9898598210", "date": "2021-01-01 09:39:13", "md5": "627c68f2b5a6e6b899b77fb76997eefd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "H20818_1.fq.gz", "size": "9501519978", "date": "2021-01-01 10:18:54", "md5": "65c318fa82f92e7a52a9acfce8a9183c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]