Human Developing Kidney Spatial Transcriptomic Datasets (seqFISH)
收藏资源简介：
These supplementary data contain additional raw and processed seqFISH files quantifying 246 genes from three human developing kidney samples. The raw microscopy data are not uploaded owing to their large size, but are available upon reasonable request (Nils Lindström: nils.lindstrom@med.usc.edu, Connor C. Fausto: cfausto@usc.edu). ROI1 - Week 13.5 (Generated 2024_04_20) | -- roi1_wk13p5-CF_2024_04_20-CellCoordinates.csv contains XY coordinates for every cell in the dataset. | -- roi1_wk13p5-CF_2024_04_20-CellxGene.csv contains a CellxGene matrix for the quantity of transcripts in each cell (determined after segmentation). | -- roi1_wk13p5-CF_2024_04_20-TranscriptList.csv contains a matrix with each row containing information regarding mRNA transcript detected, it's XY coordinate, and the z-slice detected. ROI2 - Week 16.5 (Generated 2024_04_20) | -- roi2_wk16p5-CF_2024_04_20-CellCoordinates.csv contains XY coordinates for every cell in the dataset. Note that 9.71 units in this coordinate system is 1 micron. | -- roi2_wk16p5-CF_2024_04_20-CellxGene.csv contains a CellxGene matrix for the quantity of transcripts in each cell (determined after segmentation). | -- roi2_wk16p5-CF_2024_04_20-TranscriptList.csv contains a matrix with each row containing information regarding mRNA transcript detected, it's XY coordinate, and the z-slice detected. | -- Hu_Kidney_wk16p5_seqFISH_2024_04_20_Seurat-v2.rds contains a Seurat object made from the raw data, with spatially mapped metadata from an early nephron and collecting duct subset snRNA-seq object (Kim et al., Dev Cell 2024) ROI6 - Week 16.5 (Generated 2024_10_16) | -- roi6_wk16p5-CF_2024_10_16-CellCoordinates.csv contains XY coordinates for every cell in the dataset. | -- roi6_wk16p5-CF_2024_10_16-CellxGene.csv contains a CellxGene matrix for the quantity of transcripts in each cell (determined after segmentation). | -- roi6_wk16p5-CF_2024_10_16-TranscriptList.csv contains a matrix with each row containing information regarding mRNA transcript detected, it's XY coordinate, and the z-slice detected. Additional files | -- md5sums.txt contains checksums for each file Modifications 2024-10-30 First submission. This dataset is for a pre-print, and will be made publically available upon manuscript publication. 2026-06-15 Published with an embargo. Files will be made public upon journal publication.
