EXPERIMENT_TITLE: Illumina HiSeq 2500 paired end sequencing; Promoter capture Hi-C of CD34+ haematopoietic stem cells
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Bone marrow was collected from patients undergoing total hip replacement (in a consented study approved by the London-Westminster Research Ethics Committee - IRAS:220344). Samples were treated with granulocyte colony-stimulation factor (G-CSF) to mobilise CD34+ cells from the bone marrow. Cells were diluted with 4 volumes of PBS with 2mM EDTA and centrifuged at 300g for 10 mins at room temperature to pellet them. The pellet was washed twice with PBS-EDTA, finally resuspended in 50ml PBS and transferred to 500 ml DMEM supplemented with 10% FBS. Cells were fixed by the addition of 26ml of 37% formaldehyde to a final concentration of 2% and fixed for 10 mins. Fixation was quenched with glycine at a 0.125M final concentration. Capture Hi-C was performed following the protocol in Mifsud et al. 2015, with the minor modification of in situ ligation instead of in solution ligation. Promoter interactions were enriched using the linked biotynilated RNA bait library. Following the Hi-C library enrichment for promoter interactions, a post-capture PCR amplification was carried out using PE PCR 1.0 and PE PCR 2.0 primers with 4 to 6 PCR amplification cycles. Using Illumina TruSeq library preparation kit.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: CD34+ heamatopoietic stem cells were isolated from the bone marrow of two healthy donors undergoing total hip replacement. Promoter capture Hi-C (PCHi-C) was performed on these cells using the protocol according to  Mifsud et al. 2015, with the exception that ligation was performed in situ, and a slightly modified bait capture set was used. Bait positions in hg19 are included as an additional file.
SAMPLE_TITLE: CD34_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA first public", "VALUE": "2021-08-01"}, {"TAG": "ENA last update", "VALUE": "2021-08-01"}, {"TAG": "External Id", "VALUE": "SAMEA9362457"}, {"TAG": "INSDC center alias", "VALUE": "College of Health and Life Sciences, Hamad Bin Khalifa University"}, {"TAG": "INSDC center name", "VALUE": "College of Health and Life Sciences, Hamad Bin Khalifa University"}, {"TAG": "INSDC first public", "VALUE": "2021-08-01T00:18:18Z"}, {"TAG": "INSDC last update", "VALUE": "2021-08-01T00:18:18Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "E-MTAB-10701:CD34_rep2"}, {"TAG": "broker name", "VALUE": "ArrayExpress"}, {"TAG": "cell type", "VALUE": "CD34-positive, CD38-negative hematopoietic stem cell"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "developmental stage", "VALUE": "adult"}, {"TAG": "genotype", "VALUE": "wild type genotype"}, {"TAG": "individual", "VALUE": "2"}, {"TAG": "organism part", "VALUE": "bone marrow"}, {"TAG": "sample name", "VALUE": "E-MTAB-10701:CD34_rep2"}, {"TAG": "sampling site", "VALUE": "hip joint"}]
Pool_Member_@attributes_sample_title: CD34_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: CD34_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR6212994.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/ERR006/6212/ERR6212994/ERR6212994.lite.1", "size": "24080630204", "date": "2022-07-30 13:41:23", "md5": "facca8b5d6e55bc138b77a3159c23479", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ERR6212994", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR6212994/ERR6212994", "size": "37111309608", "date": "2021-11-12 03:41:58", "md5": "f3e8c24f4b5cd14d6cba4f7ee2e2d4e7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CD34-rep2_R2.fastq.gz", "size": "29796426979", "date": "2021-11-12 03:20:39", "md5": "2d74e01662c656fe997a9f002478dbf2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CD34-rep2_R1.fastq.gz", "size": "28085805303", "date": "2021-11-12 02:58:24", "md5": "05a778e5f6e7a50c2fbbaa5f70ac47d1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]