GEO DataSets

(Submitter supplied) We report the effect of cryopreservation on isolated microglia and macrophages from the brains of rhesus monkeys. At the time of necropsy, cells were isolated from the brain and either used fresh or cryopreserved. For single cell sequencing, isolates were purified for CD11b expression and captured and processed through the 10xGenomics platform following by sequencing. We find that cryopreservation altered the expression of approximately 2% of the genes. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29319

4 Samples

Download data: H5

(Submitter supplied) Single nucleus RNA-Seq (snRNA-Seq) is used as an alternative to single cell RNA-Seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-Seq is able to detect cellular state in human tissue. Indeed, snRNA-Seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer’s Disease. Our comparison of microglia from single cells and single nuclei of four human subjects revealed that, while the majority of genes showed similar relative abundances in cells and nuclei, a small population of genes (~1%) was depleted in nuclei compared to whole cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TSV

(Submitter supplied) Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing. We introduce single-nucleus RNA-sequencing as an alternative approach for investigating human islets.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: CSV

(Submitter supplied) Human pancreatic islets, including insulin secreting beta-cells are a major focus of transplantation strategies aimed at identifying new therapeutic approaches to counteract hyperglycemia in patients with diabetes. Identifying the transcriptomic signature of human islet cells provides insights into regulatory pathways that can be harnessed for planning therapeutic strategies. In this context, single-cell RNA-sequencing (scRNA-seq) has been used mostly in vitro. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: CSV

(Submitter supplied) A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT

(Submitter supplied) To investigate novel markers for snRNA seq and graft in-vivo snRNA seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: CSV

(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) Microglia are the tissue macrophages of the central nervous system (CNS) and the first to respond to CNS dysfunction and disease. Gene expression profiling of microglia during development, under homeostatic conditions and in the diseased CNS provided insight in microglia functions and changes thereof. Single cell sequencing studies further contributed to our understanding of microglia heterogeneity in relation to age, sex and CNS disease. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

22 Samples

Download data: CSV, MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2446 Samples

Download data

(Submitter supplied) We generated single-cell RNAseq profiles of microglia and brain myeloid cells (1922 total; 1816 cells passed quality control) from different developmental stages (E14.5, P7 and P60) to study their heterogeneity. Cells were isolated from either the whole developing brain (for the E14.5 stage) or six separate regions (for P7 and P60 stages): Cortex (CTX), Cerebellum (CB), Hippocampus (HIP), Striatum (STR), Olfactory bulb (OB), Choroid plexus (CP). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1922 Samples

Download data: CSV

(Submitter supplied) We generated single-cell RNAseq profiles of 143 microglia, sorted in the gate CD45lowCD11+Gpnmb+Clec7a+, from postnatal day 7 cerebellum to validate the newly identified “proliferative region-associated microglia (PAM)” (Gpnmb and Clec7a are PAM surface markers). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

143 Samples

Download data: CSV

(Submitter supplied) We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

369 Samples

Download data: CSV

(Submitter supplied) To compare microglial regional heterogeneity, we generated bulk RNA-seq profiles of postnatal day 60 microglia, sorted by TMEM119+ (also CD45lowCD11b+), from cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR) regions. For each sample, 3000 microglia were FACS sorted into RLT lysis buffer for total RNA extraction, followed by Smart-seq library preparation and Illumina Nextseq (sequence depth 10-20 million per sample). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(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:

Homo sapiens; Mus musculus; Drosophila melanogaster

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) 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) 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) 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:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22396

8 Samples

Download data: MTX, TSV