GEO DataSets

(Submitter supplied) In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.

Organism:

Pseudomonas aeruginosa; Klebsiella pneumoniae; Enterococcus faecalis; Escherichia coli

Type:

Expression profiling by high throughput sequencing

5 related Platforms

35 Samples

Download data: TSV, TXT

(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) We present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline. We demonstrated that PETRI-seq effectively barcoded single bacterial cells in a species-mixing experiment with E. coli (MG1655) and S. aureus (USA300). Within the S. aureus population, we found rare prophage induction in 0.04% of cells. We further demonstrated that PETRI-seq was able to distinguish between E. more...

Organism:

Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL24034 GPL27809

18 Samples

Download data: TXT, XLSX

(Submitter supplied) Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. more...

Organism:

Saccharomyces cerevisiae; Candida albicans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26171 GPL34036

7 Samples

Download data: MTX, TSV

(Submitter supplied) Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41. We also inlcude a bulk RNA-seq study of unsorted and sorted cells using CD44 as a marker

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: MTX, TSV, 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) Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed “single-cell combinatorial fluidic indexing” (scifi). The scifi-RNA-seq assay combines one-step combinatorial pre-indexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25526 GPL24676

14 Samples

Download data: CSV, H5AD

(Submitter supplied) The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

543 Samples

Download data: TXT

(Submitter supplied) M3-Seq is a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We use M3-Seq to profile hundreds of thousands of bacterial cells and reveal rare populations of bacteria that include bet-hedging strategies, prophage induction, and phage-infected cells in E. coli and B. subtilis.

Organism:

Escherichia coli; Pseudomonas aeruginosa; Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33391 GPL33390

4 Samples

Download data: CSV

(Submitter supplied) Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells, in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. Another challenge are rare cells that need to be collected over several days, or samples prepared at different times or locations. more...

Organism:

Drosophila melanogaster; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

18 Samples

Download data: TXT

(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. “Spike-in” RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

3 Samples

Download data: MTX, RDS, TXT

(Submitter supplied) Massively parallel single cell RNA-seq (scRNA-seq) for diverse applications, from cell atlases to functional screens, is increasingly limited by sequencing costs, and large-scale low-cost sequencing can open many additional applications, including patient diagnostics and drug screens. Here, we adapted and systematically benchmarked a newly developed, mostly-natural sequencing by synthesis method for scRNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

16 Samples

Download data: CSV, H5, TXT

(Submitter supplied) To test if scRNA-seq contains sufficient phylogenetic information to reconstruct a population history of cancer, immunosuppressed NU/J mice were injected with human cancer cells (MDA-MB-231-LM2). The tumors that develop are derived from the same population and thus share a common ancestor, but evolved independently in each mouse and should form separate clades on reconstructed phylogenetic trees when analysed together. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: H5

(Submitter supplied) Single cell RNA sequencing so far only depicts cellular transcriptomes at a single time point with low temporal resolution for kinetic changes. Here, we present a single-cell approach based on metabolic RNA labelling for combined sequencing of total and newly transcribed RNA as well as computational analysis of the RNA present prior to labelling. We apply it to cytomegalovirus infection of fibroblasts and reveal its potential for delineating alterations in transcriptional activity and decay in single cells under perturbed experimental conditions.

Organism:

Mus musculus; Murid betaherpesvirus 1; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25867 GPL19057 GPL25526

124 Samples

Download data: H5, TSV, TXT

(Submitter supplied) Single-cell RNA-seq measurements of the normal mouse bone marrow cells using inDrop protocol

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: CSV

(Submitter supplied) Gene expression profiling via RNA-sequencing has become standard for measuring and analyzing the gene activity in bulk and at single cell level. Increasing sample sizes and cell counts provides substantial information about transcriptional architecture of samples. In addition to quantification of expression at cellular level, RNA-seq can be used for detecting of variants, including single nucleotide variants and small insertions/deletions and also large variants such as copy number variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: MTX, TSV

(Submitter supplied) We performed large-scale single-cell RNA-seq on human iPSCs subjected to endothelial cell differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: RDA, TXT

(Submitter supplied) We found that single-cell RNA-seq (scRNA-seq)dataneeded to have2,000or more cellsin a cluster to identify the majority of differentially expressed genes (DEGs) with modest differences, while as few as 50-100cells weresufficient for identifying the majority of DEGs withextremely small p values or high abundance.The findings provide a quantitativereference for designing and interpreting studies that usescRNA-seq datato identify DEGs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV, TXT