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| Status |
Public on May 25, 2022 |
| Title |
0902 Macula Choroid |
| Sample type |
SRA |
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| Source name |
Choroid
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| 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: 3430
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Nov 05, 2021 |
| Last update date |
May 25, 2022 |
| Contact name |
Dwight Edward Stambolian |
| E-mail(s) |
stamboli@pennmedicine.upenn.edu
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| Phone |
2158980305
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| Organization name |
University of Pennsylvania
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| Department |
Opthalmalogy
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| Lab |
Stellar-Chance 313
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| Street address |
422 Curie Blvd.
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE188280 |
Single Cell RNA-Seq of normal and AMD eyes |
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| Relations |
| BioSample |
SAMN22930008 |
| SRA |
SRX13009800 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5676881_0902mCho_barcodes.tsv.gz |
18.2 Kb |
(ftp)(http) |
TSV |
| GSM5676881_0902mCho_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM5676881_0902mCho_matrix.mtx.gz |
20.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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