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Series GSE135441 Query DataSets for GSE135441
Status Public on Oct 14, 2020
Title Transcriptomes of Major Proximal-Tubule Cell-Culture Models
Organisms Didelphis virginiana; Homo sapiens; Canis lupus familiaris; Sus scrofa; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose:Cultured cell lines are widely used for research in the physiology, pathophysiology, toxicology and pharmacology of the renal proximal tubule. The lines that are most appropriate for a given use depend on the genes expressed.We have used modern RNA-sequencing techniques to identify the gene expression profile of 14 different cell lines plus primary cultures of mouse proximal tubule and compare them to transcriptomes of native kidney proximal tubules.
Methods: 14 different proximal tubule cell lines were grown on permeable supports under conditions specific for the respective lines. RNA-Seq followed standard procedures.
Results and conclusion: Transcripts expressed in cell lines showed variable match to transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45%) with pig kidney cells (LLC-PK1) close behind (39%). Much lower percentage matches were seen for various human lines including HK-2 cells (26%) and lines from rodent kidneys (18-23%).An online resource ( has been created for interrogation of the data.No cell line closely matched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particular metabolic and transport processes seen in the proximal tubule.
Overall design We provide a web-based resource that allows users to compare expression of specific transcripts across all cell lines and to download data for deeper analysis.
Contributor(s) Khundmiri SJ, Chen L, Lederer E, Yang CR, Knepper MA
Citation(s) 33122286
Submission date Aug 06, 2019
Last update date Sep 14, 2021
Contact name Lihe Chen
Phone 3015947152
Organization name NHLBI
Street address 10 center drive MSC 1603, Building 10, Room 6N318
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (6)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
GPL23945 Illumina HiSeq 3000 (Rattus norvegicus)
Samples (43)
GSM4009040 WKY,transcriptome 01
GSM4009041 WKY,transcriptome 02
GSM4009042 WKY,transcriptome 03
BioProject PRJNA558898
SRA SRP217532

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135441_Human_Cells.txt.gz 2.0 Mb (ftp)(http) TXT
GSE135441_LLC-PK1_Cells.txt.gz 589.8 Kb (ftp)(http) TXT
GSE135441_MDCK_Cells.txt.gz 598.0 Kb (ftp)(http) TXT
GSE135441_Mouse_Cells.txt.gz 971.9 Kb (ftp)(http) TXT
GSE135441_OK_cells.txt.gz 793.3 Kb (ftp)(http) TXT
GSE135441_Primary_mPT.txt.gz 772.6 Kb (ftp)(http) TXT
GSE135441_Rat_Cells.txt.gz 890.8 Kb (ftp)(http) TXT
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