CNSA: a data repository for archiving omics data

Guo, Xueqin; Chen, Fengzhen; Gao, Fei; Li, Ling; Liu, Ke; You, Lijin; Hua, Cong; Yang, Fan; Liu, Wanliang; Peng, Chunhua; Wang, Lina; Yang, Xiaoxia; Zhou, Feiyu; Tong, Jiawei; Cai, Jia; Li, Zhiyong; Wan, Bo; Zhang, Lei; Yang, Tao; Zhang, Minwen; Yang, Linlin; Yang, Yawen; Zeng, Wenjun; Wang, Bo; Wei, Xiaofeng; Xu, Xun

doi:10.1093/database/baaa055

Cited by 300 publications

(216 citation statements)

References 16 publications

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“…The data that support the findings of this study have been deposited into CNGB Sequence Archive (CNSA) [64] of China National GeneBank DataBase (CNGBdb) [65] with accession number CNP0001218.…”

Section: Supplementary Informationmentioning

confidence: 98%

Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

Sun

Wang

et al. 2021

Cell Biosci

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Background Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, much more remains to be characterized in the developmental origin, cell fate determination, and identity of human LSCs. The lack of knowledge hindered the establishment of efficient differentiation protocols for generating hPSC-derived LSCs and held back their clinical application. Results Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells (hESCs). Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hESCs-derived LSCs and their progeny—the transit amplifying cells. Conclusion Single-cell RNA-seq revealed time-course expression changes and significant transcriptional heterogeneity during hESC-derived LSC differentiation in vitro. Our results demonstrated candidate developmental trajectory and several new candidate markers for LSCs, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.

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Section: Supplementary Informationmentioning

confidence: 98%

Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

Sun

Wang

et al. 2021

Cell Biosci

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“…Slides were scanned immediately using a dual-channel scanner (Genepix 4000B). The microarray raw data have been deposited into CNGB Sequence Archive (Guo et al, 2020) of CNGBdb (Chen et al, 2020) with accession number CNP0001267.…”

Section: Microarray Hybridizationmentioning

confidence: 99%

Pediatric Acute Lymphoblastic Leukemia Patients Exhibit Distinctive Alterations in the Gut Microbiota

Liu

Zou

Ruan

et al. 2020

Front. Cell. Infect. Microbiol.

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Previous studies have shown that gut microbiota can affect human immune system in many ways. Our aim was to investigate quantitative differences in fecal bacterial compositions of childhood acute lymphoblastic leukemia (ALL) patients compared to those of healthy children, so as to identify individual bacterial species that are related to the etiology of ALL. We recruited 81 subjects, including 58 patients with ALL and 23 healthy controls. Fecal samples were collected and examined by 16S rRNA quantitative arrays and bioinformatics analysis. Both Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional scaling (NMDS) demonstrated that the microbial composition of ALL patients deviated from the tight cluster of healthy controls. Multiple bacterial species exhibited significant changes (e.g., Roseburia faecis, Edwardsiella tarda, and Fusobacterium naviforme) in the ALL samples. Some of the differentially abundant taxa were correlated with the level of interleukin-10. The ALL cases could be efficiently distinguished from healthy controls by the random forest model based on differential species (area under ROC curve = 0.843). Taken together, the composition of gut microbiota differed from healthy controls to pediatric ALL patients. Our study identified a series of ALL-related species in the gut microbiota, providing a new direction for future studies aiming to understand the host-gut microbiota interplay in ALL pathogenesis.

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“…All supporting data and materials are available in the GigaScience GigaDB database [ 71 ]. The data reported in this study are also available in the CNGB Sequence Archive (CNSA) [ 72 ] of China National GeneBank DataBase (CNGBdb) [ 73 ] with accession No. CNP0001417.…”

Section: Data Availabilitymentioning

confidence: 99%

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

et al. 2020

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Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.

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CNSA: a data repository for archiving omics data

Cited by 300 publications

References 16 publications

Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

Pediatric Acute Lymphoblastic Leukemia Patients Exhibit Distinctive Alterations in the Gut Microbiota

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

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