EXPERIMENT_TITLE: Illumina HiSeq 2500 paired end sequencing
STUDY_DESCRIPTOR_STUDY_ABSTRACT: HIC sequencing data has been generated for 1KG trios and the reads are mapped to grch38. Interaction matrices are calculated for each chromosome which lets us view the chromatin interactions inside the organisms. Hi-C data was generated for the thousand genomes project SV group by the laboratory of Bing Ren. under an embargo and cannot be used in independent publications until February 1, 2017. Please direct correspondence to the UCSD PIs Bing Ren (biren@ucsd.edu) and Jonathan Sebat
SAMPLE_TITLE: Coriell GM19238
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "DNA-ID", "VALUE": "NA19238"}, {"TAG": "population", "VALUE": "YRI"}, {"TAG": "Super Population Code", "VALUE": "AFR"}, {"TAG": "Coriell plate", "VALUE": "HAPMAPPT03"}, {"TAG": "Coriell panel", "VALUE": "MGP00013"}, {"TAG": "Population Description", "VALUE": "Yoruba in Ibadan, Nigeria"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "HapMap sample ID", "VALUE": "NA19238"}, {"TAG": "Super Population Description", "VALUE": "African"}, {"TAG": "culture_collection", "VALUE": "CORIELL:GM19238"}, {"TAG": "Family ID", "VALUE": "Y117-02"}, {"TAG": "family_id", "VALUE": "Y117"}, {"TAG": "relationship", "VALUE": "Mother"}]
Pool_Member_@attributes_sample_title: Coriell GM19238
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Coriell GM19238
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM19238_Hi-C_biorep1_seq1_read2.fastq.bz2", "url": "http://ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR1227632/GM19238_Hi-C_biorep1_seq1_read2.fastq.bz2", "size": "2083169840", "date": "2019-09-06 15:34:51", "md5": "f8293424a4f0306bca29812e7a14648e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR1227632.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/ERR001/227/ERR1227632/ERR1227632.sralite.1", "size": "1765949077", "date": "2021-06-16 04:28:34", "md5": "0a950951b07b54659f5ca926dbc441b2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ERR1227632", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR1227632/ERR1227632", "size": "4148488523", "date": "2016-02-10 20:11:19", "md5": "14173574a2ad84fd6b7fc5f237828688", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM19238_Hi-C_biorep1_seq1_read1.fastq.bz2", "url": "http://ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR1227632/GM19238_Hi-C_biorep1_seq1_read1.fastq.bz2", "size": "2000837458", "date": "2019-09-06 15:34:51", "md5": "56d17e3e72d29b7ff8890b3ad6bf6f8a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]