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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 04, 2019 |
| Title |
Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 450,118 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.
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| Overall design |
We have 49 organoids in total. We include 4 donors (AS, ThF, N1, N2; 2 males, 2 females) at 4 timepoints: 1 replicate each at the iPSC (Day 0), 1 replicate for 2 donors (N1, N2), 2 for the other two (AS, ThF) at Day 7, 3 replicates each at Days 15 and 29. For one donor (AS), we include 2 experiments at D15 and D29. For one donor (ThF), we have extended culture experiments at D32 (3 replicates) and D51(1 replicate). For ThF, we generated D29 organoids (3 replicates) from a second protocol. We have 2 transplanted organoids at D29. Organoids were pooled on lanes using a randomized design to ensure that organoids replicates from an individual batch (donor, replicate, condition) were distributed across lanes.
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| Contributor(s) |
Subramanian A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 26, 2019 |
| Last update date |
Nov 06, 2019 |
| Contact name |
Ayshwarya Subramanian |
| E-mail(s) |
subraman@broadinstitute.org
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| Organization name |
Broad Institute
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| Department |
Klarman Cell Observatory
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
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| Samples (9)
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| GSM4044536 |
AS_ML_D29: scRNAseq data from D29 mature organoids generated from the AS line (3 replicates) |
| GSM4044537 |
AS_ML_D15: scRNAseq data from D15 organoids generated from the AS line (3 replicates X 2 experiments) |
| GSM4044538 |
AS_ML_D7: scRNAseq data from D7 organoids generated from the AS line (3 replicates) |
| GSM4044539 |
AS_ML_D0: scRNAseq data from D0/iPSC stage |
| GSM4044540 |
TF_ML_D29: scRNAseq data from D29 mature organoids generated from the TF line (3 replicates) |
| GSM4044541 |
TF_ML_D15: scRNAseq data from D15 organoids generated from the TF line (3 replicates X 2 experiments) |
| GSM4044542 |
TF_ML_D7: scRNAseq data from D7 organoids generated from the TF line (3 replicates) |
| GSM4044543 |
TF_ML_D0: scRNAseq data from D0/iPSC stage |
| GSM4044544 |
TF_ML_D32: scRNAseq data from D32 mature organoids generated from the TF line (3 replicates) |
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| Relations |
| BioProject |
PRJNA562165 |
| SRA |
SRP219278 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136314_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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