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Sample GSM8046682 Query DataSets for GSM8046682
Status Public on Jun 12, 2024
Title RGC, experiment3, GEX, scRNA-seq
Sample type SRA
 
Source name Retina
Organism Mus musculus
Characteristics tissue: Retina
cell type: Retinal ganglion cells
genotype: Vglut2-Tdtomato-Ai9
Extracted molecule total RNA
Extraction protocol Fresh mouse retinas were dissected out from Vglut2-Tdtomato-Ai9 mice in oxygenated Ames media. Retinas are digested in papain and dissociated into single cells by manual trituration in low-ovomucoid solution. RGCs were enriched by negative-rod immunopanning using an anti-CD73 antibody. RGCs were labeled with a Thy1-APC antibody. RGCs were incubated with cholesteral-modified oligos using the 10x Genomics 3' CellPlex Kit (PN-1000261). RGCs from up to 6 retinas are pooled and resuspended in oxygenated Ames media, then enriched using FACS to isolate APC and Tdtomato positive cells. Unless specified, all steps were performed in oxygenated Ames, in the presence of Actinomycin D. All steps were also performed on individual retinas up until FACS.
Library construction was performed according to the manufacturer's instructions for the Chromium Next GEM 3' Kit v3.1
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Ma_Atlas_filtered.csv
Data processing Demultiplexing was done using the Cell Ranger Multi Pipeline (in Cell Ranger v6.1.2) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/using/multi)
Assembly: GRCm38/mm10-2020A
Supplementary files format and content: We provide a universal comma-separated values file (.csv) for the filtered expression data. We also provide unprocessed barcode/feature/matrix data per experiment and the assignment confidence table based on a cell ranger's calculation using a confidence level of 0.9.
 
Submission date Jan 30, 2024
Last update date Jun 12, 2024
Contact name Justin Ma
E-mail(s) justin.ma@bcm.edu
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
 
Platform ID GPL24247
Series (1)
GSE254587 Sample multiplexing for retinal single-cell RNA-sequencing
Relations
BioSample SAMN39674171
SRA SRX23452390

Supplementary file Size Download File type/resource
GSM8046682_Exp3_assignment_confidence_table.csv.gz 1.4 Mb (ftp)(http) CSV
GSM8046682_Exp3_barcodes.tsv.gz 4.0 Mb (ftp)(http) TSV
GSM8046682_Exp3_features.tsv.gz 254.2 Kb (ftp)(http) TSV
GSM8046682_Exp3_matrix.mtx.gz 209.4 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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