GEO DataSets

(Submitter supplied) Recently, combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomics changes associated with cell preservation and how they may bias further downstream analysis remain unknown. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22396

8 Samples

Download data: MTX, TSV

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

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22396 GPL19415 GPL18573

19 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Recently, combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomics changes associated with cell preservation and how they may bias further downstream analysis remain unknown. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19415 GPL18573

11 Samples

Download data: TXT

(Submitter supplied) Background: Interest in single-cell whole transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works, investigators have used live cells which represent several inconveniences and limitations. Some recent cell fixation methods did not work with most primary cells including immune cells. Methods: The methanol-fixation and new processing method was introduced to preserve PBMCs for single-cell RNA sequencing (scRNA-Seq) analysis on 10X Chromium platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21290

9 Samples

Download data: MTX, TSV

(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) Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

35 Samples

Download data: H5, MTX, TSV

(Submitter supplied) Background: Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

54 Samples

Download data: TXT

(Submitter supplied) We performed single-cell transcriptome analysis (using 10x genomics 3' scRNA-seq v3.1 chemistry) in the sea anemone Nematostella vectensis (Cnidaria).

Organism:

Nematostella vectensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23802

1 Sample

Download data: RDS

(Submitter supplied) Single-cell sequencing technologies are revolutionizing biology, but are limited by the need of dissociating fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a species-versatile cell dissociation approach that fixes cells  as they are being dissociated. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, can be sorted by Fluorescence-Activated Cell Sorting (FACS) and are permeable, enabling combinatorial approaches of single-cell transcriptomics. more...

Organism:

Dugesia japonica; Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28515

3 Samples

Download data: GTF, 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) 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:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

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:

GPL24676 GPL24247

3 Samples

Download data: TXT

(Submitter supplied) We report how methanol fixation influences transcriptome profile in single cell RNA-seq. We generatad Smart-seq2 data from two cell lines, and both live and fixed cells from each cell line were processed and analyzed to illustrate fixaiton effect.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

346 Samples

Download data: CSV

(Submitter supplied) With the growing interest in studying primary tissue samples by single cell transcriptome analysis, there is an emerging demand for a preservation strategy that enables sample transportation and storage. In this study, we describe a simple and general strategy that preserves primary tissues at hypothermic temperature. Using FACS and single-cell RNAseq, we demonstrated the effectiveness of this strategy in maintaining cell viability, cell population heterogeneity, and cell transcriptome integrity for primary tissues that underwent up to 3 days of preservation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

502 Samples

Download data: CSV

(Submitter supplied) We developed and validated a simple method for viable cryopreservation of whole blood, without any preprocessing, Simple prEservatioN of Single cElls (SENSE), with granulocyte depletion for generating high-quality single-cell profiles. We performed rigorous in-depth characterization of the SENSE method on clinical blood samples and compared it to the conventional multistep density-gradient isolation of peripheral blood mononuclear cells (PBMCs) method. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: MTX, TSV

(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