GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3231460 Query DataSets for GSM3231460
Status Public on Jan 24, 2020
Title Mm_retina_Input mRNA
Sample type SRA
Source name Retina (spanning 11 cell types)
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: retina
cell type: mixed sample (non-demultiplexed)
age: post natal week 10
genotype: wild type
gender: male
Extracted molecule total RNA
Extraction protocol Ten-week old wild type C57BL/6J male mouse was purchased from Jackson Laboratory (Bar Harbor, ME, USA). The mouse was sacrificed with cervical dislocation under anesthesia, and an eyeball was immediately removed and placed in cold phosphate buffered saline (PBS). The mouse retina was carefully removed under a dissecting microscope, and the retina tissue was dissociated straightaway using the Papain dissociation system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions. Briefly, the mouse retina was incubated at 37°C for 30 min in Earle's Balanced Salt Solution (EBSS) with DNase followed by tissue trituration with a 10 ml pipette. Cell pellet was collected after centrifugation at 300g for 5 minutes, and then re-suspended in DNase dilute albumin-inhibitor solution.The cell suspension was carefully layered on top of the albumin-inhibitor solution, and then centrifuged at 70g for 6 minute. Similar procedure was followed for post-morten human eye tissue Next, the cell pellet was washed and re-suspended in 1 : 1DMEM/F12 + 10% FBS. All centrifugation steps were performed at room temperature. The final cell suspension was filtered with 40 μm cell strainer (Falon, Corning, NY, USA) to remove large clump and debris. All experimental procedures approved by University of Pennsylvania Animal Care and Use Committee.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Retinal Horizontal Cells (RHCs) were identified by means of Lhx1+ and Prox1+ expression. sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer’s recommendations.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing The 10X pipeline used was Cell Ranger 2.0.0.
Seurat software was used to normalize gene counts and process the raw data
Genome_build: mm8
Supplementary_files_format_and_content: txt file (gene x cells)
Submission date Jun 28, 2018
Last update date Jan 24, 2020
Contact name Dwight Edward Stambolian
Phone 2158980305
Organization name University of Pennsylvania
Department Opthalmalogy
Lab Stellar-Chance 313
Street address 422 Curie Blvd.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL17021
Series (2)
GSE116426 Anatomical-spatial dissection of single-cell retinal transcriptomics paves the road for new horizons in complement immunology [Mm]
GSE117959 Cellular milieu of the neural retina informs complement immune regulation
BioSample SAMN09516134
SRA SRX4321487

Supplementary file Size Download File type/resource
GSM3231460_barcodes.tsv.gz 369.6 Kb (ftp)(http) TSV
GSM3231460_cell.ident.txt.gz 486.8 Kb (ftp)(http) TXT 1.1 Mb (ftp)(http) TXT
GSM3231460_genes.tsv.gz 186 b (ftp)(http) TSV
GSM3231460_matrix.mtx.gz 246.5 Kb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap