EXPERIMENT_TITLE: GSM8024400: Human kidney cortex, Hi-C, rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: We extracted nuclei from tissues and used the nuclear suspensions for library preparation (1 million nuclei for each Hi-C reaction). Hi-C library preparation was performed with the Arima Library Prep Kit v2 (A303011, Arima Genomics). Hi-C and CUT&RUN on the same nuclear suspension pool
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Here, we leveraged our recently described high-yield nuclei extraction method and performed Hi-C and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing of histone modifications (H3K4me3 and H3K27me3) in parallel on the kidney cortex, medulla and papilla samples dissected from the same donor. This site describes the Hi-C data. Overall design: Hi-C was performed with the Arima-HiC kit (A510008, Arima Genomics). Hi-C library preparation was performed with the Arima Library Prep Kit v2 (A303011, Arima Genomics). CUT&RUN was performed with the CUTANA™ ChIC / CUT&RUN Kit v3. CUT&RUN library preparation was performed with the NEBNext® Ultra™ II DNA Library Prep Kit. All 6 dual-indexed Hi-C libraries and 18 dual-indexed CUT&RUN libraries were sequenced on a 300-cycle NovaSeq X Plus platform (Illumina).
SAMPLE_TITLE: Human kidney cortex, Hi-C, rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Kidney"}, {"TAG": "tissue", "VALUE": "Kidney"}, {"TAG": "kidney region", "VALUE": "cortex"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Human kidney cortex, Hi-C, rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human kidney cortex, Hi-C, rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR27636980.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR027/27636/SRR27636980/SRR27636980.lite.1", "size": "43185531733", "date": "2024-01-19 04:41:35", "md5": "3626f6ee728058eba86a4e123847962c", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR27636980", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR27636980/SRR27636980", "size": "50949036245", "date": "2024-01-18 23:23:56", "md5": "78823062af4b7beabd5fa618aad782b0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C2_L001_R2_001.fastq.gz", "size": "42470850136", "date": "2024-01-18 23:09:29", "md5": "6a709c219139897aa863e3e564a450f6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C2_L001_R1_001.fastq.gz", "size": "41050048955", "date": "2024-01-18 23:07:59", "md5": "23202372cba41bdf1b45366bf35277ee", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]