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Series GSE126906 Query DataSets for GSE126906
Status Public on Feb 22, 2019
Title Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines 10X]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.
 
Overall design our experiment utilized the 5 human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827. For the single cell designs, the five cell lines were mixed equally and processed by 10X chromium and CEL-seq2, referred to as sc_10X_5cl, and sc_CEL-seq2_5cl respectively in analysis that follows. For CEL-seq2, three plates were sorted and processed.
 
Contributor(s) Tian L, Su S, Seidi A, Naik SH, Jabbari JS, Ritchie M
Citation(s) 30096152, 31133762
Submission date Feb 21, 2019
Last update date Dec 01, 2021
Contact name Shian Su
E-mail(s) su.s@wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Molecular Medicine
Lab Ritchie Lab
Street address 1G Royal Parade
City Melbourne
State/province Victoria
ZIP/Postal code 3052
Country Australia
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (1)
GSM3618014 H2228_H1975_A549_H838_HCC827_Mixture_10X
This SubSeries is part of SuperSeries:
GSE118767 Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods
Relations
BioProject PRJNA523629
SRA SRP186515

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Supplementary file Size Download File type/resource
GSE126906_RAW.tar 17.7 Mb (http)(custom) TAR (of CSV)
GSE126906_barcodes.csv.gz 44.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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