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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 25, 2024 |
| Title |
Ctrl-3 |
| Sample type |
SRA |
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| Source name |
Murine retinal endothelial cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Murine retinal endothelial cells
age: P17
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell populations were isolated from mouse retinal, In brief, the tissue was incubated in dissociation buffer containing 1 mg/ml hyaluronidase（sigma,H3506） and 20,000U/ml DNase I（sigma,DN25） for 15 min at 37 C. Enzymatic digestion was quenched with Dulbecco’s Modifified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, 10270106, Gibco). Cells were resuspended at a concentration of 1 million cells per ml and stained with PBST containing 1% FCS
P17 mouse retinal tissue were enzymatically dissociated as described above and 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000-9000 cells. Cell populations were isolated from mouse retinal. Retinas of the eyes of two mice were taken at a time The Chromium Single Cell 3’Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3’Reagent Kits User Guide Version 3. Libraries were sequenced on Illumina novaseq 6000 using paired-end 150 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
The replication 3 for Ctrl group of adult mice was subjected to a normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.
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| Data processing |
P17 mouse retinal tissue were enzymatically dissociated as described above and 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000-9000 cells. Cell populations were isolated from mouse retinal. Retinas of the eyes of two mice were taken at a time The Chromium Single Cell 3’Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3’Reagent Kits User Guide Version 3. Libraries were sequenced on Illumina novaseq 6000 using paired-end 150 bp.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
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| Submission date |
Apr 22, 2021 |
| Last update date |
Nov 25, 2024 |
| Contact name |
sen da XIE |
| E-mail(s) |
[email protected]
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| Phone |
18860051556
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| Organization name |
Zhongshan ophthemology center
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| Street address |
54 Xianlie Road
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| City |
Guangzhou，China |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL30028 |
| Series (1) |
| GSE173079 |
Rising from the dead: A novel mechanism involving pyroptosis and pathologic neovascularization in retinopathy of prematurity |
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| Relations |
| BioSample |
SAMN18592724 |
| SRA |
SRX10538879 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5259472_Ctrl-3_barcodes.tsv.gz |
40.0 Kb |
(ftp)(http) |
TSV |
| GSM5259472_Ctrl-3_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM5259472_Ctrl-3_matrix.mtx.gz |
27.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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