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Single cell RNA-Seq atlas of the developing murine retina

10x single cell RNA-seq data from the developing mouse retina

Developed as a joint project between the following labs: Loyal Goff - www.gofflab.org Seth Blackshaw - Blackshaw Lab Elana Fertig - https://fertiglab.com/

Primary contact for dataset: Loyal Goff [email protected]

Use agreement

Although these data are being made publicly available as part of the CZI Computational Tools working group, the producers consider these data as unpublished and expect that the data will be used in accord with standard scientific etiquette and practices concerning unpublished data. Researchers are encouraged to use these data exclusively for the development of novel methods to analyze scRNA-Seq related to cell-cell variation, trajectory analysis and cell type identification/characterization. Use of these data for other purposes requires the explicit consent of the creators prior to an embargo date of July 1st, 2018 or the public release of the associated preprint.

Stats

Sample/Batches

Age Replicate Number Cells
E11 1 8301
E12 1 1503
E14 2 24206
E16 1 4763
E18 2 20578
P0 1 8873
P2 2 15582
P5 1 5366
P8 2 10200
P14 1 7680

Count Matrix

The count matrix is provided in .mtx format and can be downloaded here: 10x_mouse_retina_development.mtx

Cellular Phenotype Data

10x_mouse_retina_development_phenotype.csv

barcode sample age Size_Factor num_genes_expressed Total_mRNAs CellType raw_cluster umap_cluster umap_coord1 umap_coord2 umap_coord3 umap_CellType used_for_pseudotime
E11.AAACCTGAGATGTAAC.1 E11.AAACCTGAGATGTAAC-1 E11 E11 1.733370 1549 2794 RPCs 32 130 3.581455 -4.245770 -3.752502 Early RPCs FALSE
E11.AAACCTGAGGCAATTA.1 E11.AAACCTGAGGCAATTA-1 E11 E11 2.201144 1848 3548 RPCs 9 103 2.634151 -5.016845 -3.926956 Early RPCs FALSE
E11.AAACCTGAGTAGCGGT.1 E11.AAACCTGAGTAGCGGT-1 E11 E11 2.381057 1935 3838 RPCs 24 130 3.268848 -3.967177 -3.942664 Early RPCs FALSE
E11.AAACCTGAGTGGAGTC.1 E11.AAACCTGAGTGGAGTC-1 E11 E11 2.861238 2139 4612 RPCs 9 115 3.737625 -4.926516 -4.012058 Early RPCs TRUE
E11.AAACCTGCAAGTTGTC.1 E11.AAACCTGCAAGTTGTC-1 E11 E11 2.044805 1723 3296 Lens Epithelia 74 77 3.857854 -4.027292 -2.717437 Early RPCs FALSE
E11.AAACCTGCACCCATTC.1 E11.AAACCTGCACCCATTC-1 E11 E11 2.280553 1806 3676 RPCs 32 109 3.386985 -3.678844 -2.939268 Early RPCs TRUE

Feature Data

10x_mouse_retina_development_feature.csv

id gene_short_name num_cells_expressed mean_expr sd_exprs bcv percent_detection
ENSMUSG00000051951 ENSMUSG00000051951 Xkr4 253 0.0021191 0.046522355 481.95455 0.2094302
ENSMUSG00000089699 ENSMUSG00000089699 Gm1992 4 0.0000331 0.005754187 30200.24999 0.0033111
ENSMUSG00000102343 ENSMUSG00000102343 Gm37381 58 0.0004801 0.021906392 2081.84482 0.0480117
ENSMUSG00000025900 ENSMUSG00000025900 Rp1 11816 0.1694811 0.635347014 14.05333 9.7811331
ENSMUSG00000109048 ENSMUSG00000109048 Rp1 0 0.0000000 0.000000000 NaN 0.0000000
ENSMUSG00000025902 ENSMUSG00000025902 Sox17 108 0.0016225 0.077612551 2288.30757 0.0894010