Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8782000.fastq.gz | Fastqsanger.gz | |||
| SRR8782001.fastq.gz | Fastqsanger.gz | |||
| SRR8782002.fastq.gz | Fastqsanger.gz | |||
| SRR8782003.fastq.gz | Fastqsanger.gz | |||
| SRR8781995.fastq.gz | Fastqsanger.gz |
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Project description:Airway basal stem cells (BSCs) in chronic lung diseases accumulate memories to promote disease-specific pathogenesis. Whether acute lung infection also endows BSCs with an inflammatory memory to impair epithelial regeneration is unknown. Here, we derived multiple BSC lines from patients with and without COVID-19 (CoV19) using tracheal aspirate (TA) as a viable source of bronchial BSCs. While tested negative for SARS-CoV-2, BSC lines from CoV19 patients bore a proinflammatory gene signature, exhibited early cell cycle exist, and displayed goblet cell hypoplasia following differentiation in air-liquid interface (ALI). These phenotypes reproduced, at least partially, changes in BSCs in patients with CoV19 assessed by bioinformatic analysis of preexisting single cell transcriptomes of BSCs and by staining of lung sections for select markers. Such a memory in BSCs previously exposed to CoV19 was mediated by increases in chromosomal accessibility at key inflammatory gene loci associated with gene dysregulation and sustained STAT3 activation. Blockade of STAT3 hyperactivation in CoV19-exposed BSCs restored mucociliary differentiation in ALI. Taken together, BSCs acquire an epigenetic memory of CoV19 to impair epithelial regeneration. BSC derivation from TA provides a versatile approach to model airway epithelium in health and lung diseases.
2023-06-01 | GSE212410 | GEO
Project description:Airway basal stem cells (BSCs) in chronic lung diseases accumulate memories to promote disease-specific pathogenesis. Whether acute lung infection also endows BSCs with an inflammatory memory to impair epithelial regeneration is unknown. Here, we derived multiple BSC lines from patients with and without COVID-19 (CoV19) using tracheal aspirate (TA) as a viable source of bronchial BSCs. While tested negative for SARS-CoV-2, BSC lines from CoV19 patients bore a proinflammatory gene signature, exhibited early cell cycle exist, and displayed goblet cell hypoplasia following differentiation in air-liquid interface (ALI). These phenotypes reproduced, at least partially, changes in BSCs in patients with CoV19 assessed by bioinformatic analysis of preexisting single cell transcriptomes of BSCs and by staining of lung sections for select markers. Such a memory in BSCs previously exposed to CoV19 was mediated by increases in chromosomal accessibility at key inflammatory gene loci associated with gene dysregulation and sustained STAT3 activation. Blockade of STAT3 hyperactivation in CoV19-exposed BSCs restored mucociliary differentiation in ALI. Taken together, BSCs acquire an epigenetic memory of CoV19 to impair epithelial regeneration. BSC derivation from TA provides a versatile approach to model airway epithelium in health and lung diseases.
2023-06-01 | GSE212411 | GEO
Project description:The bundle sheath cells (BSCs) layer – a presumed control point for radial transport of water and solutes between the vasculature and the leaf mesophyll cells (MCs) – is still largely understudied. Using isolated protoplasts, we found that 45% of the 90 genes differentially expressed in BSCs vs. MCs are membrane related and 20% are transport related, suggesting unique functionality of membrane transport in the BSCs, supported also by functional assays (electrophysiology and fluorescence imaging). A tight control of long distance transport is required for the optimization of the hydro-mineral homeostasis of organs in plants under fluctuating ambient conditions. The mechanism of ion selectivity and absorption from the xylem to the leaf is still poorly understood. The bundle sheath (BS), tightly enwrapping the leaf vasculature, has been suggested as a part of this mechanism, acting as a selective barrier which regulates the radial transport of water and solutes from the xylem to leaf cells. This suggestion relies on the anatomy, as well as on the recent physiological transport assays of the BS and its cells (BSCs). We hypothesized that the unique transport functionality of the BSCs is manifested in its transcriptome. To test this, we compared the transcriptomes of individually hand-picked protoplasts of GFP-labeled BSCs and non-labeled mesophyll cells (MCs) of Arabidopsis thaliana leaves. Indeed, in conformation of our hypothesis, 45% of the 90 genes differentially expressed in BSCs vs. MCs are membrane related and 20% are transport related, with the proton-pump AHA2 as a prominent example. Moreover, fluorescence imaging using the potentiometric dye (di-8 ANEPPS) revealed a more negative membrane potential of the BSCs protoplasts compared to those of MCs, and electrophysiological assays (patch-clamp) showed that the major, AKT2-like, membrane K+ conductances of BSCs and MCs had different voltage dependency ranges. Combined, these differences are compatible with an expected possibility of simultaneous but oppositely directed transmembrane K+ fluxes in BSCs and MCs in otherwise similar conditions.
2017-10-22 | GSE85463 | GEO
Project description:small RNA seqencing of pig small inteseine cells samples from different groups in different generations to search for weaning effect on gene expression.
2020-09-30 | GSE137087 | GEO
Project description:Glioma is the most common type of intracranial tumor and accounts for 75% of malignant brain tumors. Glioblastoma (GBM) is the most malignant form of glioma, with strong invasive capabilities and a high relapse rate even after treatment. Here, our RNA seqencing analysis of BV2 cells treated by H2O2 and si-Nr4a2 reveal the effect of oxdiative stress and Nr4a2-knockdown on phenotype of microglia. Chip-seqencing andlysis of BV2 cells by anti-Nr4a2 antibody is to find the target genes regulated by Nr4a2. Overall, our results reveal that Nr4a2 as the major transcription factors for microglia involved in immunosuppression of glioma.
2023-01-08 | GSE185759 | GEO