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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 14, 2024 |
| Title |
Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease |
| Organisms |
Homo sapiens; Mus musculus; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We developed novel chemically defined recipe media named NPSR-v2, that was capable of expanding mouse and human nephron progenitor cells (NPC) for long term culture in vitro in 2D (2 Dimension) format. NPSR-v2 and these expanded NPC can be used for versatile application, such as reprograming, whole genome-wide CRISPR screen, kidney-associated disease modeling and library drug screening etc.
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| Overall design |
Comparative gene expression profiling analysis of RNA-seq data for NPSR-v2 long-term cultured mouse and human nephron progenitor cells and primary mouse and human nephron progenitor cells. We performed bulk RNA-Seq analysis using hNPC signature genes to explore the similarity among reprogrammed iNPCLCs, cultured iNPCs (in v2) and primary hNPCs. To investigate the mechanism underlying the reprogramming of podocytes into iNPCLCs with hNPSR-v2 medium, podocytes cultured with hNPSR-v2 were collected at time-course for bulk RNA-Seq analysis. And nephron organoids derived following the advanced nephron organoids induction protocol were collected at time-course for bulk RNA-Seq analysis to investigate the iNPC-derived nephron organoids development process.
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| Contributor(s) |
Huang B, Zeng Z, Li Z |
| Citation(s) |
38692273 |
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| Submission date |
Apr 26, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Zhongwei Li |
| E-mail(s) |
zhongwei.li@med.usc.edu
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| Phone |
323-442-0296
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| Organization name |
University of Southern California
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| Department |
Keck medicine
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| Lab |
Zhongwei Li's lab
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| Street address |
1425 San Pablo St
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (4)
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| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (63)
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| GSM7232894 |
mNPC, V2, 2D, Day22, biol rep 1 |
| GSM7232895 |
mNPC, V2, 2D, Day22, biol rep 2 |
| GSM7232896 |
mNPC, V2, 2D, Day44, biol rep 1 |
| GSM7232897 |
mNPC, V2, 2D, Day44, biol rep 2 |
| GSM7232898 |
mNPC, V2, 3D-2D, biol rep 1 |
| GSM7232899 |
mNPC, V2, 3D-2D, biol rep 2 |
| GSM7232900 |
CRISPR screen plasmid Lib |
| GSM7232901 |
CRISPR screen, biol rep 1 |
| GSM7232902 |
CRISPR screen, biol rep 2 |
| GSM7232903 |
hNPC, V1, 2D, Day15, Biol rep 1 |
| GSM7232904 |
hNPC, V1, 2D, Day15, Biol rep 2 |
| GSM7232905 |
hNPC, V1, 2D, Day15, Biol rep 3 |
| GSM7232906 |
iNPC, V1, 2D, Day15, Biol rep 1 |
| GSM7232907 |
iNPC, V1, 2D, Day15, Biol rep 2 |
| GSM7232908 |
iNPC, V1, 2D, Day15, Biol rep 3 |
| GSM7232909 |
hNPC, V2, 2D, Day16 |
| GSM7232910 |
iNPC, V2, 2D, Day17 |
| GSM7232911 |
hNPC, V2, 2D, Day30 |
| GSM7232912 |
iNPC, V2, 2D, Day30 |
| GSM7232913 |
hNPC, V2, 2D, Day52 |
| GSM7232914 |
iNPC, V2, 2D, Day55 |
| GSM7232915 |
hNPC, V2, 2D, Day80 |
| GSM7232916 |
iNPC, V2, 2D, Day80 |
| GSM7232917 |
iNPC, SIX2+, Day0, biol rep 1 |
| GSM7232918 |
iNPC, SIX2+, Day0, biol rep 2 |
| GSM7232919 |
iNPC, SIX2+/PAX2+, Day0, biol rep 1 |
| GSM7232920 |
iNPC, SIX2+/PAX2+, Day0, biol rep 2 |
| GSM8007268 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D3 iNPC-derived nephron organoids, replicate 1 |
| GSM8007269 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D3 iNPC-derived nephron organoids, replicate 2 |
| GSM8007270 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D5 iNPC-derived nephron organoids, replicate 1 |
| GSM8007271 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D5 iNPC-derived nephron organoids, replicate 2 |
| GSM8007272 |
SIX2- cells, isolated from D7 iNPC-derived nephron organoids, replicate 1 |
| GSM8007273 |
SIX2- cells, isolated from D7 iNPC-derived nephron organoids, replicate 2 |
| GSM8007274 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 1 |
| GSM8007275 |
D13 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 2 |
| GSM8007276 |
D19 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 1 |
| GSM8007277 |
D19 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 2 |
| GSM8007278 |
D2 iNPC-derived nephron organoid, replicate 1 |
| GSM8007279 |
D2 iNPC-derived nephron organoid, replicate 2 |
| GSM8007280 |
D4 iNPC-derived nephron organoid, replicate 1 |
| GSM8007281 |
D4 iNPC-derived nephron organoid, replicate 2 |
| GSM8007282 |
D7 iNPC-derived nephron organoid, replicate 1 |
| GSM8007283 |
D7 iNPC-derived nephron organoid, replicate 2 |
| GSM8007284 |
D10 iNPC-derived nephron organoid, replicate 1 |
| GSM8007285 |
D10 iNPC-derived nephron organoid, replicate 2 |
| GSM8007286 |
D14 iNPC-derived nephron organoid, replicate 1 |
| GSM8007287 |
D14 iNPC-derived nephron organoid, replicate 2 |
| GSM8007288 |
D21 iNPC-derived nephron organoid, replicate 1 |
| GSM8007289 |
D21 iNPC-derived nephron organoid, replicate 2 |
| GSM8007290 |
SIX2-/PODXL+ podocytes, isolated from D7 iNPC-derived nephron organoids, replicate 1 |
| GSM8007291 |
SIX2-/PODXL+ podocytes, isolated from D7 iNPC-derived nephron organoids, replicate 2 |
| GSM8007292 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 2 days, replicate 1 |
| GSM8007293 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 2 days, replicate 2 |
| GSM8007294 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 4 days, replicate 1 |
| GSM8007295 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 4 days, replicate 2 |
| GSM8007296 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 6 days, replicate 1 |
| GSM8007297 |
SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 6 days, replicate 2 |
| GSM8007298 |
D9 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1 |
| GSM8007299 |
D9 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2 |
| GSM8007300 |
D16 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1 |
| GSM8007301 |
D16 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2 |
| GSM8007302 |
D24 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1 |
| GSM8007303 |
D24 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2 |
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| Relations |
| BioProject |
PRJNA962184 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230707_CRISPR_screen_beta_scores_All_genes_.xlsx |
1.8 Mb |
(ftp)(http) |
XLSX |
| GSE230707_Normalized_sgRNA_read_counts_in_CRISPR_screen.xlsx |
3.9 Mb |
(ftp)(http) |
XLSX |
| GSE230707_Partek_iNPCs_Normalized_TMM.xlsx |
11.2 Mb |
(ftp)(http) |
XLSX |
| GSE230707_hNPC_DESeq2_Medium_ratio.xlsx |
7.0 Mb |
(ftp)(http) |
XLSX |
| GSE230707_mNPC_DESeq2_Medium_ratio.xlsx |
3.3 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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