EXPERIMENT_TITLE: GSM6519807: Neurons D868N Hi-C #1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For in situ Hi-C libraries preparation 5 milions of either NPCs or neurons were used. An already published experimental protocol was used 4. The procedures consist in different experimental steps: (i) crosslinking cells with formaldehyde at 1% concentration, (ii) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnI) within intact permeabilized nuclei, (iii) filling in and biotinylating the resulting 5′-overhangs, (iv) ligating the blunt ends, (v) shearing the DNA, (vi) pulling down the biotinylated ligation junctions with streptavidin beads, and (vii) analyzing these fragments using paired end sequencing. A first sequencing run of 5 milion reads perform to verify the experimental quality. After passing the quality check, sample were sequenced paired end on Nova-seq6000 at San Raffaele hospital omics facility. TruSeq
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To understand the effect of SET protein accumulation on genomic function we used different accumulating models, cells and in vivo, that we analyzed with different techinques up to the single level. SET accumulation is known to be caused by the accumulation of its direct interactor SETBP1, when mutated, the causative gene of Schinzel Giedion syndrome. SET has been shown to be able to interfere with histones acetylation, thus we wanted to investigated the functional effect on the genome function and cell fate commitment. Overall design: Genomic analysis of human cells (IPSCs, NPCs, Neurons), Zebrafish brain embryo, mouse embryonic and post natal cortex, to understand the effect of SET accumulation on genome function
SAMPLE_TITLE: Neurons D868N Hi-C #1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NPC-derived Neurons"}, {"TAG": "cell type", "VALUE": "NPC-derived Neurons"}, {"TAG": "genotype", "VALUE": "SETBP1 D868N"}]
Pool_Member_@attributes_sample_title: Neurons D868N Hi-C #1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Neurons D868N Hi-C #1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR21307395.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR021/21307/SRR21307395/SRR21307395.lite.1", "size": "38626431589", "date": "2023-05-10 21:56:52", "md5": "0d76a0f160c60d8825d8f193e9c98dd3", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR21307395", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21307395/SRR21307395", "size": "51618589501", "date": "2022-08-31 05:34:32", "md5": "a4236e5408bc3a90e50dc81eee981d4b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Neu_D868N_1_R2.fastq.gz", "size": "40594857684", "date": "2022-08-31 05:19:56", "md5": "308c7cade15607b1bf07b7e7f928d197", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Neu_D868N_1_R1.fastq.gz", "size": "38983997681", "date": "2022-08-30 19:14:49", "md5": "5bf51a5d3ffdf744ee3835172137204e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]