EXPERIMENT_TITLE: GSM7267210: Noness, Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: According to Arima Hi-C kit for Mammalian cell lines manual (A160134 v01). In brief, the crosslinked cells were lysed, and then underwent restriction enzymatic digestion, biotin integration, and proximal ligation. The ligated DNA was finally captured with AMPure XP beads. According to NEBNext Ultra II DNA Library Prep (Arima, A160141 v01). In brief, the proximally-ligated genomic DNA was sheared to 200-600 bp (average 400 bp) on a Covaris Ultrasonicator, and then biotin enrichment was performed using streptavidin beads, followed by end repair, dA-tailing, and adapter ligation. Arima Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: HUB162 (chr11:42,878,450-42,883,450, hg38) was identified as an essential locus in the quiescent region in the K562 cells, and HUB161 (chr11:42,873,450-42,878,450, hg38) as a nonessential one. We used Arima Hi-C to study chromosomal structure after CRISPR-Cas9 deletion of either HUB162 (Ess) or HUB161 (Noness) Overall design: K562 cells stably-expressing Cas9 (mCherry) were infected with pgRNA-expressing lentivirus (EGFP) and then cultured for 10 days. GFP+/mCherry+ cells were sorted and Hi-C was performed according to Arima Hi-C kit for Mammalian cell lines user guide (A160134 v01)
SAMPLE_TITLE: Noness, Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "blood"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell line", "VALUE": "K562"}, {"TAG": "cell type", "VALUE": "Lymphoblast"}, {"TAG": "genotype", "VALUE": "HUB161-KO"}, {"TAG": "restriction enzyme", "VALUE": "Arima (multi-enzyme)"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "pw_noness_S1_L004_R2_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR24376211/pw_noness_S1_L004_R2_001.fastq.gz.1", "size": "73591971998", "date": "2023-05-01 13:53:26", "md5": "c564db416e3a1964b564c04e669f01d0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "pw_noness_S1_L004_R1_001.fastq.gz", "url": "https://sra-pub-src-2.s3.amazonaws.com/SRR24376211/pw_noness_S1_L004_R1_001.fastq.gz.1", "size": "70071827366", "date": "2023-05-01 13:58:15", "md5": "e2edd1a322231235348877b1a7dbefe0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]