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Series GSE254587 Query DataSets for GSE254587
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
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.
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.
Contributor(s) Ma J, Chu TK, Polo-Prieto M, Park Y, Li Y, Chen R, Mardon G, Frankfort B, Tran N
Citation(s) 38812536
Submission date Jan 30, 2024
Last update date Jun 13, 2024
Contact name Justin Ma
Organization name Baylor College of Medicine
Department ophthalmology
Lab NC304
Street address 1 Baylor Plaza, Baylor College of Medicine
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (11)
GSM8046677 RGC, experiment0, non-multiplex, scRNA-seq
GSM8046678 RGC, experiment1, GEX, scRNA-seq
GSM8046679 RGC, experiment1, CMO-multiplex, scRNA-seq
BioProject PRJNA1071096

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE254587_Ma_Atlas_filtered.csv.gz 122.4 Mb (ftp)(http) CSV
GSE254587_RAW.tar 1.5 Gb (http)(custom) TAR (of CSV, MTX, TSV)
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Raw data are available in SRA

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