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| Status |
Public on Feb 27, 2023 |
| Title |
Robustness of Single-cell RNA-Seq for Identifying Differentially Expressed Genes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We found that single-cell RNA-seq (scRNA-seq)dataneeded to have2,000or more cellsin a cluster to identify the majority of differentially expressed genes (DEGs) with modest differences, while as few as 50-100cells weresufficient for identifying the majority of DEGs withextremely small p values or high abundance.The findings provide a quantitativereference for designing and interpreting studies that usescRNA-seq datato identify DEGs.
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| Overall design |
We performed scRNA-seq and poly(A)-dependent bulk RNA-seq in comparable aliquots of human induced pluripotent stem cells (iPSC)-derived, purifiedvascular endothelial and smooth muscle cells.
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| Contributor(s) |
Liu Y, Huang J, Pandey R, Liu P, Qiu Q, Liang M |
| Citation(s) |
37394518 |
| BioProject |
PRJNA938085 |
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| Submission date |
Feb 27, 2023 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Jing Huang |
| E-mail(s) |
jinghuang800@gmail.com
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| Organization name |
Medical College of Wisconsin
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| Street address |
8701 W Watertown Plank Rd
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| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (12)
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| GSM7066037 |
VSMC, replicate 1, bulk RNA-seq |
| GSM7066038 |
VSMC, replicate 2, bulk RNA-seq |
| GSM7066039 |
VSMC, replicate 3, bulk RNA-seq |
| GSM7066040 |
EC, replicate 1, scRNA-seq |
| GSM7066041 |
EC, replicate 2, scRNA-seq |
| GSM7066042 |
EC, replicate 3, scRNA-seq |
| GSM7066043 |
VSMC, replicate 1, scRNA-seq |
| GSM7066044 |
VSMC, replicate 2, scRNA-seq |
| GSM7066045 |
VSMC, replicate 3, scRNA-seq |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE226163_RAW.tar |
92.8 Mb |
(http)(custom) |
TAR (of CSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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