GEO DataSets

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the ongoing pandemic of coronavirus disease 2019 (COVID-19). Single cell RNA sequencing (scRNAseq) studies have been valuable for studying SARS-CoV-2 pathogenesis, but the performance of these methods to detect and quantify viral RNAs has not been evaluated. Here we develop an analysis pipeline, single cell coronavirus sequencing (scCoVseq), to quantify unambiguous reads derived from coronavirus genomic (gRNA) and subgenomic mRNAs (sgmRNAs). more...

Organism:

Homo sapiens; Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22096 GPL18573

11 Samples

Download data: CSV, H5, RDS

(Submitter supplied) Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High-throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a pathogenic mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) We employed an experimental design where PBMCs from a single donor was sequenced with or without mixing with PBMCs from other healthy unrelated donors in order to determine whether PBMCs engage in an allogeneic response under standard scRNA-seq sample preparation conditions (e.g., 30 minute co-incubation at 4C)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL15520

10 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Single cell RNA-seq was used to profile gene expression in 5 human lung adenocarcinoma cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: CSV, GFF3

(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TAR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

396 Samples

Download data

(Submitter supplied) In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol (MATQ-seq), providing enhancements that achieve a higher cell throughput while also including integration of automation. We selected a more efficient reverse transcriptase which led to a lower drop-out rate and higher workflow robustness, and we also successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

384 Samples

Download data: TSV

(Submitter supplied) In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol (MATQ-seq), providing enhancements that achieve a higher cell throughput while also including integration of automation. We selected a more efficient reverse transcriptase which led to a lower drop-out rate and higher workflow robustness, and we also successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30637

12 Samples

Download data: TSV

(Submitter supplied) To understand the immune response and cellular characteristics of individuals with persistent pulmonary symptoms after COVID-19 infection, single-cell RNA sequencing was performed on peripheral blood mononuclear cells from both control and pulmonary post-acute sequelae of SARS-CoV-2 (PPASC) participants. Increased myeloid-lineage cells and up-regulated genes associated with pulmonary symptoms and fibrosis were observed in PPASC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: MTX, TSV

(Submitter supplied) Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. more...

Organism:

Homo sapiens; Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL29682

12 Samples

Download data: MTX, TSV

(Submitter supplied) Detailed knowledge about dynamics of SARS-CoV-2 infection in vivo is important for unraveling the viral and host response factors that contribute to COVID-19 pathogenesis. The unknown dose and exposure timing in human infections makes the needed well-controlled time course studies impossible and thus animal models of disease are essential to fill in the gaps in our understanding of disease progression. more...

Organism:

Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29061

20 Samples

Download data: TAR

(Submitter supplied) Healthy human peripheral blood mononuclear cells (PBMCs) investigated with 10x Genomics single cell RNA-sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: H5

(Submitter supplied) SARS-CoV-2 has caused a historic pandemic of respiratory disease (COVID-19) and current evidence suggests severe disease is associated with dysregulated immunity within the respiratory tract1,2. However, the innate immune mechanisms that mediate protection during COVID-19 are not well defined. Here we characterize a mouse model of SARS-CoV-2 infection and find that early CCR2-dependent infiltration of monocytes restricts viral burden in the lung. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(Submitter supplied) We used single cell RNA sequencing (scRNA-seq) to investigate the SARS-CoV-2 RNA dissemination.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

3 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: Numerous viruses manipulate the host translation machinery and specifically block host mRNA translation. The goal of this study is to define the translational landscape of SARS-CoV-2 and SARS-CoV-2 infected cells using a combination of RNA-seq and ribo-seq approches, the latter being a powerful proxy for protein-level changes. Methods: Vero E6 and primary human bronchial epithelial cells were infected with SARS-CoV-2 at varying multiplicities of infection and followed throughout early and late phases of infection. more...

Organism:

Chlorocebus sabaeus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL11154 GPL28836

156 Samples

Download data: TXT

(Submitter supplied) We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. more...

Organism:

Drosophila melanogaster; Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

20 Samples

Download data: BW, TAR, TSV

(Submitter supplied) Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data because cell abundancy might affect to the network. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq), a scRNA-seq method that relied on terminator, terminal transferase, and nanowell/beads-based scRNA-seq platform, that could acquire scRNA-seq data with higher correlation with flow-cytometric data, gene-detection sensitivity, and robustness than widely-used methods.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

5 Samples

Download data: TXT

(Submitter supplied) Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data because cell abundancy might affect to the network. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq), a scRNA-seq method that relied on terminator, terminal transferase, and nanowell/beads-based scRNA-seq platform, that could acquire scRNA-seq data with higher correlation with flow-cytometric data, gene-detection sensitivity, and robustness than widely-used methods.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: TXT

(Submitter supplied) Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data because cell abundancy might affect to the network. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq), a scRNA-seq method that relied on terminator, terminal transferase, and nanowell/beads-based scRNA-seq platform, that could acquire scRNA-seq data with higher correlation with flow-cytometric data, gene-detection sensitivity, and robustness than widely-used methods.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

3 Samples

Download data: TXT