EXPERIMENT_TITLE: GSM5100390: HiC in iNeuron rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) DNA digestion using MboI, (3) filling in and marking ends with Biotin, (4) proximity ligation, (5) DNA shearing, (6) pulling down the biotinylated ligation junctions with streptavidin beads, and (7) paired end sequencing. As quality control (QC), we confirmed efficient restriction, ligation and DNA shearing with an agarose DNA gel and for appropriate size selection in using Agilent 4200 TapeStation system after steps (5) and (6). For the final QC, we performed 75 paired end sequencing on the Illumina Nextseq to assess quality of the libraries based on percent of Intra-chromosomal reads, long Range (>20Kb) reads, and Library Complexity. The HiC libraries were sequenced on 100 paired end sequencing using Illumina Novaseq 6000.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breakage at specific sites within the genome. Genome-wide mapping reveals that these single-strand breaks (SSBs) are located within enhancers at or near to CpG dinucleotides and sites of DNA demethylation, and are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair elevate the extent of DNA repair synthesis at neuronal enhancers, whereas deficiencies in long-patch repair reduce synthesis, suggesting that the high steady-state level of SSB repair in neuronal enhancers is sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell type-specific SSB repair, revealing unexpected levels of localized and continuous DNA single-strand breakage in neurons. In addition, these data suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair. Overall design: We developed synthesis-associated with repair sequencing (SAR) to detect DNA repair in postmotitic neuron cells. Combined with ChIP-seqs, SEAL-seq, END-seq and HiC, we were able to study the DNA damage and its repair mechansim in neurons.
SAMPLE_TITLE: HiC in iNeuron rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "iNeuron"}, {"TAG": "harvested day", "VALUE": "day7"}, {"TAG": "cell type", "VALUE": "neuron differentiated from iPSC"}]
Pool_Member_@attributes_sample_title: HiC in iNeuron rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC in iNeuron rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13764831.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13764/SRR13764831/SRR13764831.lite.1", "size": "3007098623", "date": "2022-07-27 22:44:48", "md5": "0925a78f0525b667333712a1e06b28d3", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13764831", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13764831/SRR13764831", "size": "4482916455", "date": "2021-02-22 16:58:12", "md5": "b9dec308ad65f953f55fd19077ea345b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "iNeuron_HiC_rep1_R2.fastq.gz", "size": "3691956210", "date": "2021-02-22 16:52:05", "md5": "99161daa90ebf9c66dd92ce363632409", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "iNeuron_HiC_rep1_R1.fastq.gz", "size": "3617100291", "date": "2021-02-22 16:54:16", "md5": "26de825e5ac224beb1b959718b254f3a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]