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Series GSE230707 Query DataSets for GSE230707
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
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.
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.
Contributor(s) Huang B, Zeng Z, Li Z
Citation(s) 38692273
Submission date Apr 26, 2023
Last update date Jun 13, 2024
Contact name Zhongwei Li
Phone 323-442-0296
Organization name University of Southern California
Department Keck medicine
Lab Zhongwei Li's lab
Street address 1425 San Pablo St
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platforms (4)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (63)
GSM7232894 mNPC, V2, 2D, Day22, biol rep 1
GSM7232895 mNPC, V2, 2D, Day22, biol rep 2
GSM7232896 mNPC, V2, 2D, Day44, biol rep 1
BioProject PRJNA962184

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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
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Raw data are available in SRA
Processed data are available on Series record

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