EXPERIMENT_TITLE: GSM4873936: Myelogenous leukemia cell line - K562; s5; Ma. et. al 2018 this paper; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: K562 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration. DNAse Hi-C was performed as described in (Ma. et. Al 2018) DNase Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Hi-C technique is widely used to study 3-dimensional chromatin architecture and assemble genomes. Conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in non-uniform genomic coverage. Using sequence-agnostic restriction enzymes such as DNAse I could overcome this limitation. Here we compared different DNAse Hi-C protocols and identified several critical steps which significantly impact protocol efficiency. We proposed a new robust protocol for preparation of DNAse Hi-C libraries, supplemented with experimental controls and computational pipeline for evaluation of libraries quality and data analysis. Overall design: DNase Hi-C (Ma. et. al 2018 this paper) assay in the peripheral blood of humans (7 samples), and in k562 cell line (1 sample). DNase Hi-C (Ma. et. al 2018 with non homologous blunt and bridge adapters) assay in the peripheral blood of humans (3 samples), and in k562 cell line (1 sample). DNase Hi-C (Ma. et. al 2018 with single long linker) assay in the peripheral blood of humans (1 sample), and in k562 cell line (1 sample). DNase Hi-C (Romani et al. with biotin-fillin) assay in the peripheral blood of humans (9 samples), and in k562 cell line (1 sample). DNase Hi-C (Romani et al. with single long linker) assay in the peripheral blood of humans (3 samples). DNase Hi-C (Romani et al. with Ma. et. al linker) assay in the peripheral blood of humans (1 sample). We neither used data produced by Romani et al., nor we collaborated with Dr. Romani to produce our data. The aim of our study is to compare several protocols, and we used the protocol described in Romani et al.  paper. Thus, the title "Romani et al." here refers to the specific protocol used for samples preparation. *** Submitter declares that they do not have permission to deposit the raw data (for samples s1-s4, s6-s11, s13-s29, s31-s32) due to patient privacy concerns.
SAMPLE_TITLE: Myelogenous leukemia cell line - K562; s5; Ma. et. al 2018 this paper
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Myelogenous leukemia cell line"}, {"TAG": "cell line", "VALUE": "K562 cells"}, {"TAG": "extract_protocol", "VALUE": "As described in (Ma. et. Al 2018)"}]
Pool_Member_@attributes_sample_title: Myelogenous leukemia cell line - K562; s5; Ma. et. al 2018 this paper
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Myelogenous leukemia cell line - K562; s5; Ma. et. al 2018 this paper
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "k562_exoc_s5_R1.fastq.gz", "size": "79858042", "date": "2020-10-30 10:42:40", "md5": "e2fad0f264792f4b19d4fa326da10e4a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "k562_exoc_s5_R2.fastq.gz", "size": "85268812", "date": "2020-10-30 10:42:38", "md5": "31e56625e850d0db08e6a62fd6881781", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12951752", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12951752/SRR12951752", "size": "133510277", "date": "2020-10-30 10:42:50", "md5": "d99c2790319c8594e139677f281d80bf", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12951752.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR012/12951/SRR12951752/SRR12951752.lite.1", "size": "75522805", "date": "2022-07-21 00:06:09", "md5": "32d968ce4a3a11806b368afed210d6fe", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]