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| Status |
Public on Jun 30, 2024 |
| Title |
RS5 |
| Sample type |
SRA |
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| Source name |
differentiated iPSC cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: differentiated iPSC cells
cell line: iPSC
cell type: retinal sheet
treatment: differentiated for 5 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
RS cells were freshly collected from the plates, resuspended in a dissociation buffer to obtain single cells, and then strained to ensure analysis of only single cells. Viability was determined by staining for live cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, RS cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: loupe files produced by Cell Ranger 7.0.1
Supplementary files format and content: h5 files produced by Cell Ranger 7.0.1
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| Submission date |
Mar 28, 2023 |
| Last update date |
Jun 30, 2024 |
| Contact name |
Gilbert Bernier |
| Organization name |
HMR
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| Lab |
Gilbert Bernier
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| Street address |
5690 rosemont boulevard
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T 2H2 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE228436 |
Transplantation of human iPSC-derived cone photoreceptor sheets in the sub-retinal space of a minipig model of severe photoreceptor degeneration |
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| Relations |
| BioSample |
SAMN33956774 |
| SRA |
SRX19800540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7120682_RS5cloupe.cloupe.gz |
99.9 Mb |
(ftp)(http) |
CLOUPE |
| GSM7120682_RS5filtered_feature_bc_matrix.h5 |
31.0 Mb |
(ftp)(http) |
H5 |
| GSM7120682_RS5raw_feature_bc_matrix.h5 |
66.7 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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