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| Status |
Public on Jun 12, 2024 |
| Title |
Sample multiplexing for retinal single-cell RNA-sequencing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Single cell RNA sequencing (ScRNA-seq) often requires sample pooling, but sample variance is rarely addressed. We perform scRNA-seq on retinal ganglion cells with retina-multiplexing to assess the whether this enables comparisons between retinas of an experiment.
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| Overall design |
Retinal ganglion cells (RGCs) of Vglut2-Tdtomato-Ai9 mice were enriched and isolated by negative-rod immunopanning using an anti-CD73 antibody and Fluorescence-Activated Cell Sorting (FACS) selecting for positivity of a Thy1-APC antibody and Tdtomato expression. Cholesterol-modified-oligos were used during RGC isolation for multiplexing. Samples were prepared and sequenced with the use of the 10x Genomics 3' chromium platform.
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| Contributor(s) |
Ma J, Chu TK, Polo-Prieto M, Park Y, Li Y, Chen R, Mardon G, Frankfort B, Tran N |
| Citation(s) |
38812536 |
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| Submission date |
Jan 30, 2024 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Justin Ma |
| E-mail(s) |
justin.ma@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
ophthalmology
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| Lab |
NC304
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| Street address |
1 Baylor Plaza, Baylor College of Medicine
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (11)
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| GSM8046677 |
RGC, experiment0, non-multiplex, scRNA-seq |
| GSM8046678 |
RGC, experiment1, GEX, scRNA-seq |
| GSM8046679 |
RGC, experiment1, CMO-multiplex, scRNA-seq |
| GSM8046680 |
RGC, experiment2, GEX, scRNA-seq |
| GSM8046681 |
RGC, experiment2, CMO-multiplex, scRNA-seq |
| GSM8046682 |
RGC, experiment3, GEX, scRNA-seq |
| GSM8046683 |
RGC, experiment3, CMO-multiplex, scRNA-seq |
| GSM8046684 |
RGC, experiment4, GEX, scRNA-seq |
| GSM8046685 |
RGC, experiment4, CMO-multiplex, scRNA-seq |
| GSM8046686 |
RGC, experiment5, GEX, scRNA-seq |
| GSM8046687 |
RGC, experiment5, CMO-multiplex, scRNA-seq |
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| Relations |
| BioProject |
PRJNA1071096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE254587_Ma_Atlas_filtered.csv.gz |
120.5 Mb |
(ftp)(http) |
CSV |
| GSE254587_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of CSV, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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