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In this study, we performed a time series single-cell transcriptome experiment on Arabidopsis root explants that were induced on CIM (callus induction medium) for 0 day (CIM0), 1 day (CIM1), and 4 days (CIM4), and constructed a detailed single-cell transcriptional map of callus induction process. Based on this atlas, we successfully identified a cell type that responsible for the initiation of early callus: lateral root primordia-initiating like (LRPI-like) cells, and inferred their developmental trajectory. Further analysis found that LRPI-like cells is composed of cell subtypes at multiple developmental states which exhibited distinct pluripotency features, which revealed a cell lineage map of callus initiation. In addition, the transcription factor regulatory network analysis for LRPI-like cells revealed a number of transcription factors and their target genes involved in regulating the development of LRPI-like cells, such as LRP1. Collectively, the construction of cell lineage map of callus initiation gives unique glimpse of cell fate transition during callus formation, and these will further facilitate the identification of crucial regulators that promote callus formation.

Previous studies have highlighted the importance of mitochondria dynamic in the pathogenesis of PD. Dynamin-1-like (DNM1L) is a gene encodes for dynamin-related protein 1 (DRP1), a GTPase essential for proper mitochondria fission. Here we evaluated the relationship between DNM1L variants and PD in Chinese population. A total of 3879 PD patients and 2931 healthy controls were recruited and genotyped by whole-exome sequencing and whole-genome sequencing.

Whole transcriptome sequencing data of accessory gonad tissue in Eriocheir sinensis

Three-generation full-length transcriptome of Elymus sibiricus

The miRNA data of Eriocheir sinensis accessory gland tissue

USH2A variant identified in a Han-Chinese patient with clinically suspected retinitis pigmentosa.

Compare with negative shallow-HRD status, positive shallow-HRD status presented favorable progression-free survival after being treated with PARPis. ShallowHRD status is a good biomarker for predicting prognosis, which could help guide the clinical application of PARPis in ovarian cancer patients by a cost-effective, time and data-storage saving method.

Gemcitabine plus cisplatin (GP) chemotherapy is the standard of care for nasopharyngeal carcinoma (NPC). However, the mechanisms underpinning its clinical activity are unclear. Using single-cell RNA sequencing and T and B cell receptor sequencing of matched, treatment-naive and post-GP chemotherapy NPC samples, we identified that GP chemotherapy activated an innate-like B cell (ILB)-dominant antitumor immune response. Collectively, our study provides a high-resolution map of the tumor immune microenvironment after GP chemotherapy and uncovers a role for B cell-centered antitumor immunity. We also identify and validate ILB as a potential biomarker for GP-based treatment in NPC, which could improve patient management.

The project data included RNA sequencing data from tobacco treated with four S concentrations at three different time periods.

Transcriptome sequencing was performed on soybean seeds treated with cadmium stress and control group

identification of the key cell composition and key regulatory genes of bovine horn bud tissue by bulk transcriptome and single cell transcriptome sequencing data during the development of bovine horn embryo.

Sepsis; Lipid-Metabolism; Machine learning algorithm; Single-cell RNA sequencing; Metabolomics

This project uses spatiotemporal multi-omics technology to construct spatiotemporal mapping of human embryonic organs within 3 to 8 weeks after fertilization, excavate the mechanisms of embryo development process at different stages, explore the development process of embryos and other major basic scientific research issues.

Exosomal miRNA data of adult and juvenile crabs in Eriocheir sinensis

In this study，we discovered and characterized 3 de novo mutations in KCNH5 that potentially caused a severe conditions observed in 3 Chinese children.

The study investigated changes in gut microbiota composition in patients with acute coronary syndrome (ACS) before and after treatment. The study identified specific bacteria, genes, and metabolic pathways that may be associated with cardiovascular disease risk and found that the gut microbiota of patients returned to a relatively stable state one month after treatment. This study may provide insights into the underlying mechanisms of ACS and to identify potential therapeutic targets. Specifically, the identification of specific bacteria, genes, and metabolic pathways that may be associated with cardiovascular disease risk could lead to the development of targeted interventions and treatments for ACS.

The red swamp crayfish Procambarus clarkii (Girard, 1852), native to the southern United States and northern Mexico, has attracted considerable research attention owing to its importance in aquaculture, as well as its significant ecological impact as an invasive species. Here, we present a chromosome-scale genome assembly for P. clarkii, generated using a combination of Illumina, PacBio and Hi-C sequencing. To address these key questions related to its invasion success, we performed detailed analyses of the genome organization and the evolution of gene families implicated in feeding, detoxification and immunity.

the data of T7_HotMPS_PE100_WGS_NA12878_PCR_PCRfree and T7_HotMPS_PE100_WES_NA12878

Fecal metagenome and metabolites of Grus nigricollis

The spine has essential roles in supporting body weight, and safely passaging the neural elements between the body and the brain. In this study, we used integrated single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing analyses to reveal the cellular heterogeneity, linage, and transcriptional regulatory network of the developing human spine. We found that EPYC+HAPLN1+ fibroblasts with stem cell characteristics could differentiate into chondrocytes by highly expressing the chondrogenic markers ACAN and COL2A1. Neurons could originate from neuroendocrine cells, and MEIS2 may be an essential transcription factor that promotes spinal neural progenitor cells to selectively differentiate into neurons during early gestation. Furthermore, the interaction of NRP2_SEMA3C and CD74_APP between macrophages and neurons may be essential for spinal cord development. Our integrated map provides a blueprint for understanding human spine development in the early- and midgestational stages at single-cell resolution and offers a tool for investigating related diseases.

Combined analysis of non-human primate basal ganglia cell atlases and regulatory networks using single-cell multi-omics techniques

通过二代测序（NGS）的方法，明确一群以EGFR少见突变及TMB高的为主要特征的非小细胞肺癌患者，分析EGFR少见突变肺癌小分子抑制剂的治疗疗效

Strain genome

The sterile environment may lead to liver phenotype or function alterations, but there is a lack of systematic studies on this aspect. Therefore, this study utilized a new spatial enhanced resolution omics-sequencing (Stereo-seq) to construct spatial transcriptome (ST) profiles of germ-free (GF) and specific pathogen-free (SPF) mice liver. Combined spatial transcriptomic, single-cell transcriptomic, and metabolomic analyses identified defects in the immune system and altered fatty acid and steroid metabolic processes in the livers of GF mice at a subcellular resolution. Contribute to the understanding of the interactions between host and microbiota.

ScRNAseq data from the bone marrow cells of 14 patients with plasma cell disorder (MGUS=4, NDMM=5, RRMM=5).

基于孕妇血浆cfDNA进行高深度测序，获得胎儿基因组，并基于此基因型对胎儿进行遗传性疾病检测。

Our findings elucidated a novel mechanism of macrophage-induced anti-androgen resistance of metastatic PC and a promising therapeutic approach to treat this deadly disease.

The genome size of snake gourd was 919 Mb.The two snake gourd materials were subjected to 30X resequencing using the Illumina HiSeq platform. After whole genome resequencing, 35.76 GB and 33.18 GB of clean data were obtained from the S1 and S2 populations, respectively. The Q30 and GC values of S1 were 94% and 38%, respectively, and those of S2 were 93% and 37%, respectively. Compared with the reference genome, the similarity rate between parents and the F2 population was 91.09% to 91.58%.

Our findings suggest that L168/ILA ameliorates colorectal tumorigenesis and has the high potential to develop probiotic-based therapeutic strategies to resist CRC.

The genome size of bottle gourd was 298 Mb. The two bottle gourd materials were subjected to 30X resequencing using the Illumina HiSeq platform. The average Q30 was 92.53, and the GC content ranged from 32.06 to 32.88 %. The average alignment efficiency between the sample and the reference genome ( ZAAS _ Lsic _ 2.0 ) was 99.34 %, the average coverage depth was 26.75 X, and the genome coverage was 99.28 % ( at least one base coverage ).

Genomic Data of Chrysomyia megacephala

样本包括宫颈癌，健康人。

Eichhornia crassipes, commonly known as common water hyacinth, is one of the most notorious weeds that cause severe damage to the economy and natural ecosystems of infested areas. Here, we assembled a chromosome-level genome for E. crassipes.

We present a highly- continuous genome assembly of B. multicinctus. The genome size of B. multicinctus is 1.51Gb(Table 1). The maximal length of scaffold is 39.68M and the N50 length is 6.55M. The B. multicinctus has a GC content of 37.8%.

Whole transcriptome sequencing data of adult and juvenile testicular tissues in Eriocheir sinensis

The 318 Elymus sibiricus accessions were conducted for SLAF sequencing

The project data included RNA sequencing data from tobacco treated with four Mg concentrations at three different time periods.

肝细胞癌患者的全转录组测序

Genetic research about female infertility characterized by embryonic developmental failure.

随着GWAS位点的大量积累，对基因组变异的机制解析变得尤为重要，自从人类ENCODE计划启动，发现大多数基因组变异位于非编码调控区，影响调控元件的活性，进一步作用于基因表达。模式生物在这方面已经取得巨大进展，但农业动物方面相对落后，猪作为人类主要的肉类来源动物之一，对其基因组调控区的解析具有重大意义。

Sequncing data for egusi watermalon, including BSA-seq, RNA-seq and re-seq.

青山羊样品三代测序数据

The first complete and fully-phased diploid genome from a Han Chinese.

the neutrophils were isolated from the mice bone marrow which was wild type mice or ATPIF1 knockout mice (C57BL/6 background), and then stimulated with LPS. The neutrophils were collected for RNA-seq after 2 hours.

包括孕妇样本

Hallux valgus is a common form of foot deformity, and genetic factors contribute substantially to the pathogenesis of hallux valgus deformity. We conducted a genetic study on the structural variants underlying familial hallux valgus using whole exome sequencing approach. Twenty individuals from five hallux valgus families and two sporadic cases were included in this study. A total of 372 copy number variations were found and passed quality control filtering. Among them, 43 were only present in cases but not in controls or healthy individuals in the database of genomic variants. The genes covered by these copy number variations were enriched in gene sets related to immune signaling pathway, and cytochrome P450 metabolism. The hereditary CNVs demonstrate a dominant inheritance pattern. Two candidate pathogenic CNVs were further validated by quantitative-PCR. This study suggests that hallux valgus is a degenerative joint disease involving the dysregulation of immune and metabolism signaling pathways.

Solid tumors are complex ecosystems, and heterogeneity is a major challenge in overcoming tumor recurrence and metastasis. Uncovering the spatial heterogeneity of cell types and functional states in tumors is critical for developing effective therapeutics, especially at the invasive front of tumors, the regions where tumor cell infiltration and invasion are most active. We first characterized the tumor microenvironment of intrahepatic cholangiocarcinoma (ICC) using SpaTial-enhanced resolution omics sequencing (Stereo-seq) with nanoscale resolution. Sequential comparisons were made between normal areas, marginal areas, tumor areas, and lymph nodes.

Severe Pneumonia Caused by Chlamydia psittaci Complicated with Acute Respiratory Distress Syndrome

In this project, F2 generations were obtained by backcrossing F1 hybrids from reciprocal crosses between N. nucifera and N. lutea to their parents. The whole-genome sequencing and RNA-seq of F2 generations were analyzed in order to understand gene flow and the evolutionary history of Nelumbo through segregating alleles.

Sanger sequencing of three patients with GCK mutations