GEO series

Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp

GSE144216 Homo sapiens (human) Single-cell RNA-seq 73 samples Submitted 2020/01/25 Platform GPL16791

At a glance

Single-cell RNA-seq · human · 73 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 73 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Most single cell RNA sequencing protocols start with single cells dispersed from intact tissue. High-throughput processing of the separated cells is enabled using microfluidics platforms. However, dissociation of tissue results in loss of information about cell location and morphology and potentially alters the transcriptome. An alternative approach for collecting RNA from single cells is to re-purpose the electrophysiological technique of patch clamp recording.

Read the full summary ↓

A hollow patch pipette is attached to individual cells, enabling the recording of electrical activity, after which the cytoplasm may be extracted for single cell RNA-Seq (“Patch-Seq”). Since the tissue is not disaggregated, the location of cells is readily determined, and the morphology of the cells is maintained, making possible the correlation of single cell transcriptomes with cell location, morphology and electrophysiology. Recent Patch-Seq studies utilizes PCR amplification to increase amount of nucleic acid material to the level required for current sequencing technologies. PCR is prone to create biased libraries – especially with the extremely high degrees of exponential amplification required for single cell amounts of RNA. We compared a PCR-based approach with linear amplifications and demonstrate that aRNA amplification (in vitro transcription, IVT) is more sensitive and robust for single cell RNA collected by a patch clamp pipette.

This dataset

Open GSE144216 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE144216_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA603071 and SRA study SRP244658. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32029778) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 73 more — browse all 73 samples with per-sample file links →

Datasets on a similar topic

GSE298602 Single-cell RNA-Seq data from preeclamptic and healthy placentas 11 samples shares rna-seq, clamp
GSE293805 Single nucleus RNA-sequencing atlas of pediatric solid tumors 182 samples shares rna-seq
GSE310058 Single-nucleus transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [snRNA-seq] 149 samples shares rna-seq
GSE327167 Single-cell RNA-seq profiling of pleural mesothelioma and comparator pleural specimens 113 samples shares rna-seq
GSE327289 Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer’s Disease and Primary Tauopathies 76 samples shares rna-seq
GSE308103 Single-nucleus RNA-sequencing (snRNA-seq) analysis of normal lung tissues, precursor lung lesions and invasive lung adenocarcinomas 75 samples shares rna-seq
GSE202379 Single Nuclei RNA-Seq to map progression of non-alcoholic fatty liver disease (NAFLD) in patients II 59 samples shares rna-seq
GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.