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/ljy_Arcobacteraceae_MAGs_from_63samples_ALOHA_20230921
Description
249 of MAGs were obtained from the 63 metagenomic data of sinking particulate organic matter collected by sediment traps at abyssal depths at ALOHA (Boeuf, D., Edwards, B. R., Eppley, J. M., Hu, S. K., Poff, K. E., Romano, A. E., Caron, D. A., Karl, D. M.DeLong, E. F. (2019) Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proceedings of the National Academy of Sciences. 116, 11824-11832.). These were reassembled in this study using MetaSPAdes v3.13.0 with the settings “-k 21,33,55”.
Analysis typeDe Novo Assembly
OEZ014275
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OEZ_Ming_2212062343
Description
IgA nephropathy (IgAN) is a major cause of kidney failure worldwide. Here we investigated the contribution of genome-wide protein coding variants to IgAN risk by performing a three-stage exome chip-based association study in 8,529 IgAN patients and 23,224 healthy controls of Han Chinese ancestry. We discovered a novel rare nonsynonymous risk variant in VEGFA, and further sequencing of VEGFA revealed twice as many carriers of other rare variants in 2,148 IgAN cases compared to 2,732 controls. We also discovered a common nonsynonymous risk variant in PKD1L3, and the variant was shown to be associated with nearby HP gene expression and lower protein level by previous and current studies. However, a common loss-of-function mutation of PKD1L3 did not show any association, suggesting that HP is more likely to be a susceptibility gene for IgAN. Our discovery of VEGFA and HP has expanded understanding on the genetic basis of IgAN susceptibility.
Analysis typeOther
OEZ013225
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Processing
Analysis type
Other
OEZ013173
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superQ_PEM-seq_IGK
Description
The superQ pipeline (https://github.com/liumz93/superQ/) was used to identify the integration events. Briefly, after the adapter and low-quality sequence trimming using cutadapt (https://cutadapt.readthedocs.io/), the remaining sequences were aligned to the hg38 genome using bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/). The PCR duplication was removed by the molecular barcode.
Analysis typeReference Alignment
OEZ014269
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superQ_PEM-seq_TRB
Description
The superQ pipeline (https://github.com/liumz93/superQ/) was used to identify the integration events. Briefly, after the adapter and low-quality sequence trimming using cutadapt (https://cutadapt.readthedocs.io/), the remaining sequences were aligned to the hg38 genome using bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/). The PCR duplication was removed by the molecular barcode.
Analysis typeReference Alignment
OEZ014268
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superQ_PEM-seq_TRD
Description
The superQ pipeline (https://github.com/liumz93/superQ/) was used to identify the integration events. Briefly, after the adapter and low-quality sequence trimming using cutadapt (https://cutadapt.readthedocs.io/), the remaining sequences were aligned to the hg38 genome using bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/). The PCR duplication was removed by the molecular barcode.
Analysis typeReference Alignment
OEZ014115
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OEZ_Yan-na_2207250917
Description
Multiple genome-wide association studies (GWASs) have identified the MTMR3/HORMAD2/LIF/OSM region to be associated with IgA nephropathy (IgAN), but the causal variants, implicated genes, and altered functions are poorly understood. Here, we performed fine-mapping analyses based on the GWAS datasets consisting of 2,762 IgAN cases and 5,803 controls. We identified two variants explaining the entire GWAS signal, rs4823074 and rs16988135, both of which linked to the MTMR3 promoters in B-lymphoblastoid cells. Mendelian randomization studies suggested that the risk alleles may modulate disease susceptibility by affecting serum IgA levels through increased MTMR3 expression. Consistently, we observed elevated MTMR3 expression in PBMCs from IgAN patients. Further mechanistic studies in vitro demonstrated that MTMR3 increased IgA production dependent upon its PtdIns3P binding domain. Moreover, our study provided the in vivo functional evidence that Mtmr3−/− mice exhibited defective TLR9-induced IgA production and glomerular IgA deposition. Collectively, the present study indicated the role of MTMR3 in IgAN pathogenesis by enhancing TLR9-induced IgA immunity, and provided novel insights into using genetic data to explore a novel intervention target for IgAN.
Analysis typeOther
OEZ009584
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CryoEM
Description
CryoEM
Analysis typeDe Novo Assembly
OEZ014267
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human proteome microarray
Description
The median fluorescence signal at each site (F635_Median) was divided by the background (B635_Median) for data analysis, that is, original signal strength (I) = F635_Median/B635_Median. The median and SD of I were calculated to obtain the corrected data Z-Score (corrected signal strength) for each site. Proteins with a Z-Score greater than 2.8 were those that bind to HDCA. The mean value (I mean) represents the mean value of the original signal strength of each protein. I Mean-Ratio is the ratio between the Biotin-HDCA group and Biotin group. To call the candidates, the cutoff was set as a P value≤0.05 and I Mean-Ratio≥1.4.
Analysis typeDe Novo Assembly
OEZ014266
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OEZ_Wenyun_2307281403
Analysis type
De Novo Assembly
OEZ014264