Similar studies for GEO DataSets (Select 200218632) - GEO DataSets

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Items: 20

Select item 2002186321.

Improved bacterial single-cell RNA-seq through automated MATQ-seq [scRNA-seq]

(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

Series

Accession:: GSE218632

ID:: 200218632

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Select item 2002186332.

Improved bacterial single-cell RNA-seq through automated MATQ-seq

(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

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Series

Accession:: GSE218633

ID:: 200218633

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Select item 2002186313.

Improved bacterial single-cell RNA-seq through automated MATQ-seq [bulk RNA-seq]

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30637
12 Samples

Download data: TSV

Series

Accession:: GSE218631

ID:: 200218631

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Select item 2000789684.

Effective Detection of Variation in Single Cell Transcriptome using MATQ-seq

(Submitter supplied) We report here a new single-cell RNA-seq assay, Multiple Annealing and dC-Tailing based Quantitative single-cell RNA-seq (MATQ-seq), which provides the accuracy and sensitivity that enable the detection of transcriptional variations existing in single cells of the same type. We performed a systematic characterization of the technical noise using pool-and-split averaged single-cell samples and showed that the biological variations in single cells were observed with statistical significance.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
91 Samples

Download data: DAT, TXT

Series

Accession:: GSE78968

ID:: 200078968

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Select item 2001471555.

Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

(Submitter supplied) A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Bacteroides thetaiotaomicron VPI-5482

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL28278 GPL20056
40 Samples

Download data: CSV, WIG

Series

Accession:: GSE147155

ID:: 200147155

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Select item 2001088496.

Single-cell RNA-seq of fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls

(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

Series

Accession:: GSE108849

ID:: 200108849

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Select item 2001410187.

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

(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

Series

Accession:: GSE141018

ID:: 200141018

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Select item 2001233928.

MARS-seq2.0 an experimental and analytical pipeline for indexed sorting combined with Single-cell RNA sequencing

(Submitter supplied) Human tissues are composed of trillions of cells that populate a complex space of molecular phenotypes and functions that vary in abundance by 4-9 orders of magnitude. Relying solely on unbiased sampling to characterize cellular niches becomes non-feasible, as the marginal utility of collecting more cells is diminishing quickly. Further, in many clinical samples, the relevant cell types are scarce and efficient processing is critical. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL19415
30 Samples

Download data: TXT

Series

Accession:: GSE123392

ID:: 200123392

PubMed Similar studies SRA Run Selector

Select item 2001802379.

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

(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:: Escherichia coli; Enterococcus faecalis; Pseudomonas aeruginosa; Klebsiella pneumoniae

Type:: Expression profiling by high throughput sequencing

5 related Platforms
35 Samples

Download data: TSV, TXT

Series

Accession:: GSE180237

ID:: 200180237

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Select item 20005178310.

Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq

(Submitter supplied) Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:: GPL8269 GPL11154
59 Samples

Download data: TXT

Series

Accession:: GSE51783

ID:: 200051783

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Select item 20015487011.

Long and short-read single cell RNA-seq profiling of human lung adenocarcinoma cell lines using 10X V3 chemistry.

(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

Series

Accession:: GSE154870

ID:: 200154870

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Select item 20019745212.

Single cell RNA-seq by mostly-natural sequencing by synthesis

(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

Series

Accession:: GSE197452

ID:: 200197452

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Select item 20018990013.

Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing

(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:: Chlorocebus aethiops; Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL18573 GPL22096
11 Samples

Download data: CSV, H5, RDS

Series

Accession:: GSE189900

ID:: 200189900

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Select item 20011988814.

Single-cell RNA-seq reports growth condition-specific global transcriptomes of individual bacteria

(Submitter supplied) Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions. more...