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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).
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|
|
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
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|
|
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 |