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Sample GSM5957793 Query DataSets for GSM5957793
Status Public on Oct 18, 2022
Title 10XscRNA-seq-UiRO_2D
Sample type SRA
 
Source name hUC
Organism Homo sapiens
Characteristics cell type: hUC-derived 2D renal organoids
Treatment protocol Day 24 kidney organoids were dissociated into single cells with Accutase, followed by passing through a 40 mm filter thrice to remove cell clumps. Dissociated cells were subsequently stained with trypan blue and confirmed to have at least 80% viability.
Growth protocol hUCs were treated with cocktail medium to induce U-iIMPCs(urine cell derived intermediate mesoderm progenitor cells) from day0 to day7. Then U-iIMPCs were treated with differentiation medium to induce U-iNPCs(urine cell derived nephron progenitor cells) from day7 to day14. To generate 3D kidney organoids, the colonies were picked and re-aggregated into bigger cell clusters with 5-10 colonies per organoid using round bottom ultra-low attachment 96-well plates (Corning) at day 14. After aggregation for 24 hours, 3D kidney organoids were transferred onto the upper chamber of Transwell (Corning) for liquid-air interface culture, with daily media change was performed at the bottom chamber until day 24.
Extracted molecule total RNA
Extraction protocol A minimum of 10000 dissociated cells were loaded per well using the Fluidigm C1 Single Cell Auto Pre System for single cell capture.
single-cell RNA-seq library was prepared with Single Cell 3’ Reagent Kits v3(10x Genomics).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing scRNA-seq reads were aligned to the hg38 using STAR, then preprocessed with scanpy and Seurat
Assembly: hg38
Supplementary files format and content: barcode, genes and matrix files
 
Submission date Mar 17, 2022
Last update date Oct 20, 2022
Contact name huan chen
E-mail(s) chen_huan@grmh-gdl.cn
Organization name Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)
Street address Huangpu District
City guangzhou
ZIP/Postal code 510000
Country China
 
Platform ID GPL24676
Series (2)
GSE198840 Generation of human kidney organoids from urine cells (scRNA-Seq)
GSE198844 Generation of human kidney organoids from urine cells
Relations
BioSample SAMN26748285
SRA SRX14491542

Supplementary file Size Download File type/resource
GSM5957793_10XscRNA-seq-UiRO_2D_barcodes.tsv.gz 17.5 Mb (ftp)(http) TSV
GSM5957793_10XscRNA-seq-UiRO_2D_genes.tsv.gz 521.6 Kb (ftp)(http) TSV
GSM5957793_10XscRNA-seq-UiRO_2D_matrix.mtx.gz 275.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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