scBlood: A comprehensive single-cell accessible chromatin database of blood cells.

The advent of single cell transposase-accessible chromatin sequencing (scATAC-seq) technology enables us to explore the genomic characteristics and chromatin accessibility of blood cells at the single-cell level. To fully make sense of the roles and regulatory complexities of blood cells, it is critical to collect and analyze these rapidly accumulating scATAC-seq datasets at a system level. Here, we present scBlood (https://bio.liclab.net/scBlood/), a comprehensive single-cell accessible chromatin database of blood cells. The current version of scBlood catalogs 770,907 blood cells and 452,247 non-blood cells from ∼400 high-quality scATAC-seq samples covering 30 tissues and 21 disease types. All data hosted on scBlood have undergone preprocessing from raw fastq files and multiple standards of quality control. Furthermore, we conducted comprehensive downstream analyses, including multi-sample integration analysis, cell clustering and annotation, differential chromatin accessibility analysis, functional enrichment analysis, co-accessibility analysis, gene activity score calculation, and transcription factor (TF) enrichment analysis. In summary, scBlood provides a user-friendly interface for searching, browsing, analyzing, visualizing, and downloading scATAC-seq data of interest. This platform facilitates insights into the functions and regulatory mechanisms of blood cells, as well as their involvement in blood-related diseases.

scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

Long-term impact of accidental pollution on the distribution and risks of metals and metalloids in the sediment of the Longjiang River, China.

In January 2012, a serious accident polluted the Longjiang River with high concentrations of cadmium (Cd) and other concomitant metals and metalloids in the water. After emergency treatment (i.e., the addition of coagulants), these metals and metalloids were transferred from the water into the sediment through precipitation of the flocculent materials produced. In this study, the long-term distribution of six metals and metalloids in the sediment of the Longjiang River was investigated and their ecological risks were assessed. Approximately 1 year after the accident (i.e., late 2012), the average Cd content in the sediment of the affected sites decreased to 25.6 ± 19.5 mg/kg, which was 8 times higher than that of 3.16 ± 3.18 mg/kg in the upstream reference sites. In 2016 and 2017, the average Cd content in the sediment of the affected sites further decreased to 4.91 ± 2.23 and 6.27 ± 4.27 mg/kg, respectively. Compared with late 2012, the amounts of Zn, Pb, and Cu obviously decreased in 2016 and 2017, whereas there were no obvious differences in the As and Hg amounts during 3 years considered. Among metals and metalloids, the average contribution of Cd to the potential ecological risk index (RI) was 90%, 69%, and 70% in the affected areas in 2012, 2016, and 2017, respectively, suggesting that Cd was the most important factor affecting the ecological risk of metals in the Longjiang River. It should be noted that the average contribution of Hg to RI in the affected areas increased from 8% in 2012 to 25% and 23% in 2016 and 2017, respectively. The sequence of contribution of six elements was Cd > Hg > As>Pb > Cu ≈ Zn. A high ecological risk of metals and metalloids was found in the sediments of two reservoirs, probably owing to the barrier effect of the dam. This study will be useful for the environmental management of rivers affected by accidental pollution of metals and metalloids.

Distribution and ecological risk assessment of cadmium in water and sediment in Longjiang River, China: Implication on water quality management after pollution accident.

In early January 2012, the Longjiang River was subjected to a serious cadmium (Cd) pollution accident, which led to negatively environmental and social impacts. A series of measures of emergency treatment were subsequently taken to reduce water Cd level. However, little information was available about the change of Cd level in environmental matrices and long-term effect of this pollution accident to aquatic ecosystem. Thus, this study investigated the distribution of Cd in water and sediment of this river for two years since pollution accident, as well as assessed its ecological risk to aquatic ecosystem of Longjiang River. The results showed that it was efficient for taking emergency treatment measures to decrease water Cd concentration to below the threshold value of national drinking water quality standard of China. There was high risk (HQ > 1) to aquatic ecosystem in some of reaches between February and July 2012, but low or no risk (HQ < 1) between December 2012 to December 2013. Cd concentration in sediment in polluted reaches increased after pollution accident and emergency treatments in 2012, but decreased in 2013. During flood period, the sediment containing high concentration of Cd in Longjiang River was migrated to downstream Liujiang River. Cd content in sediment was reduced to background level after two years of the pollution accident occurrence. The study provides basic information about Cd levels in different media after pollution accident, which is helpful in evaluating the effectiveness of emergency treatments and the variation of ecological risk, as well as in conducting water management and conservation.