|
| Status |
Public on Feb 06, 2019 |
| Title |
Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Single-cell RNA sequencing (scRNA-Seq) provides a valuable platform for characterising multicellular ecosystems. Fibroblasts are a heterogeneous cell type involved in many physiological and pathological processes, but remain poorly-characterised. Analysis of fibroblasts is challenging: these cells are difficult to isolate from tissues, and are therefore commonly under-represented in scRNA-seq datasets. Here, we describe an optimised approach for fibroblast isolation from human lung tissues. We demonstrate the potential for this procedure in characterising stromal cell phenotypes using scRNA-Seq, analyse the effect of tissue disaggregation on gene expression, and optimise data processing to improve clustering quality. We also assess the impact of in vitro culture conditions on stromal cell gene expression and proliferation, showing that altering these conditions can skew phenotypes.
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| |
|
| Overall design |
mRNA profiles of human lung samples (tumour, inflamed and normal lung) from 3 patients
|
| |
|
| Contributor(s) |
Waise S, Hanley CJ |
| Citation(s) |
31270426 |
| Submission date |
Feb 05, 2019 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Sara Waise |
| E-mail(s) |
s.waise@soton.ac.uk
|
| Organization name |
University of Southampton
|
| Department |
Cancer Sciences
|
| Lab |
Experimental Pathology Group
|
| Street address |
Somers Building MP284, Southampton General Hospital, Tremona Road
|
| City |
Southampton |
| State/province |
Hampshire |
| ZIP/Postal code |
SO16 6YD |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (6)
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|
| Relations |
| BioProject |
PRJNA521040 |
| SRA |
SRP183758 |
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