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Sample GSM5676884 Query DataSets for GSM5676884
Status Public on May 25, 2022
Title 0902 Peripheral Retina
Sample type SRA
 
Source name Retina
Organism Homo sapiens
Characteristics age: 89
Sex: Male
race: Black or African American
medhx: HTN, hypothyroid, gout, sepsis, PNA, alzheimers, left hip fx, UTI, hypoglycemia (glucose 52 on admission but not treated for DM after Dr. consult), hypotension, dementia
phenotype: Early AMD
sequenced estimated number of cells: 10237
Extracted molecule total RNA
Extraction protocol The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina and RPE /choroid was carefully removed under a dissecting microscope and both tissue layers were dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.
single cell RNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing For each sample a cell by gene count matrix is provided
Genome_build: HG38
Supplementary_files_format_and_content: 10X Genomics sparse data matrix
 
Submission date Nov 05, 2021
Last update date May 25, 2022
Contact name Dwight Edward Stambolian
E-mail(s) stamboli@pennmedicine.upenn.edu
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 GPL16791
Series (1)
GSE188280 Single Cell RNA-Seq of normal and AMD eyes
Relations
BioSample SAMN22930011
SRA SRX13009803

Supplementary file Size Download File type/resource
GSM5676884_0902tRet_barcodes.tsv.gz 50.8 Kb (ftp)(http) TSV
GSM5676884_0902tRet_features.tsv.gz 297.6 Kb (ftp)(http) TSV
GSM5676884_0902tRet_matrix.mtx.gz 54.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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