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| Status |
Public on May 23, 2023 |
| Title |
An integrated organoid omics map extends modeling potential of kidney disease |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We performed gene expression profiling analysis using data obtained from RNA-seq of isolated kidney organoid spheroids collected at days 21, 25 and 29 in culture.
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| Overall design |
Bulk RNA Design: All bulk RNA samples start with 'Sample_' in their title. Kidney organoids were generated from human embryonic stem cells (UM77-2, NIH registry #0278) according to published protocol (Harder et al., JCI Insight 2019). Organoid spheroids were collected at day 21, day 25 and day 29, then lysed. RNA was extracted, and cDNA generated. Library prep and next-generation sequencing of total RNA on a NovaSeq4000 (150 bp, paired end) were carried out in the Advanced Genomics Core at the University of Michigan.
Single Cell Design: All single cell RNAseq samples start with 'D2' in their title.
Whole well organoids were treated at D23 with TNFα 5ng/ml for 24h and collected at D24. Cells were dissociated using cold active protease into single cells and 10x Genomics sequencing was performed in the Advanced Genomics Core at the University of Michigan.
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| Web link |
https://zenodo.org/records/8404609
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| Contributor(s) |
Eddy S, Alakwaa F |
| Citation(s) |
37580326 |
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| Submission date |
Sep 22, 2022 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Jennifer Harder |
| Organization name |
University of Michigan Medical School
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| Department |
Internal Medicine, Division of Nephrology
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| Street address |
1301 Catherine St.
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-5624 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (16)
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| GSM7168149 |
Sample_3853-JES-1, D21 Org1 |
| GSM7168151 |
Sample_3853-JES-2, D21 Org2 |
| GSM7168152 |
Sample_3853-JES-3, D25 Org1 |
| GSM7168153 |
Sample_3853-JES-4, D25 Org2 |
| GSM7168154 |
Sample_3853-JES-5, D29 Org1 |
| GSM7168155 |
Sample_3853-JES-6, D29 Org2 |
| GSM7168156 |
Sample_4372-MF-1, VC 24h |
| GSM7168157 |
Sample_4372-MF-2, TNF 24h |
| GSM7168158 |
Sample_4372-MF-3, VC 48h |
| GSM7168159 |
Sample_4372-MF-4, TNF 48h |
| GSM7211500 |
D24 Ctrl 24h |
| GSM7211501 |
D24 TNF 24h |
| GSM7211502 |
D25 NLW50 Ctrl |
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| Relations |
| BioProject |
PRJNA883395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213972_KidneyOrganoids2021_Organoids_allSamples_htseq-2234-JES_CountsGt0_voom_filtered.txt.gz |
317.6 Kb |
(ftp)(http) |
TXT |
| GSE213972_RAW.tar |
268.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
| GSE213972_Sample_3853-JES.htseq_counts_Gt0_voom_filtered.txt.gz |
787.1 Kb |
(ftp)(http) |
TXT |
| GSE213972_Sample_4372-MF.htseq_counts_Gt0_voom_filtered.txt.gz |
463.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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