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| 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
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| 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 (https://esbl.nhlbi.nih.gov/JBrowse/KCT/) 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.
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| 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.
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| 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 |
| E-mail(s) |
lihe.chen@nih.gov
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| Phone |
3015947152
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| Organization name |
NHLBI
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| Street address |
10 center drive MSC 1603, Building 10, Room 6N318
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (6)
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| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
| GPL23945 |
Illumina HiSeq 3000 (Rattus norvegicus) |
| GPL24486 |
Illumina HiSeq 3000 (Sus scrofa) |
| GPL27015 |
Illumina HiSeq 3000 (Canis lupus familiaris) |
| GPL27016 |
Illumina HiSeq 3000 (Didelphis virginiana) |
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| Samples (43)
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| GSM4009043 |
SHR,transcriptome 01 |
| GSM4009044 |
SHR,transcriptome 02 |
| GSM4009045 |
SHR,transcriptome 03 |
| GSM4009046 |
OK-WT,transcriptome 01 |
| GSM4009047 |
OKH,transcriptome 01 |
| GSM4009048 |
OKH,transcriptome 02 |
| GSM4009049 |
OKH,transcriptome 03 |
| GSM4009050 |
OK-ATCC,transcriptome 01 |
| GSM4009051 |
OK-ATCC,transcriptome 02 |
| GSM4009052 |
OK-ATCC,transcriptome 03 |
| GSM4009053 |
NRK-52E,transcriptome 01 |
| GSM4009054 |
NRK-52E,transcriptome 02 |
| GSM4009055 |
NRK-52E,transcriptome 03 |
| GSM4009056 |
MDCK,transcriptome 01 |
| GSM4009057 |
MDCK,transcriptome 02 |
| GSM4009058 |
MDCK,transcriptome 03 |
| GSM4009059 |
LLC-PK1,transcriptome 01 |
| GSM4009060 |
LLC-PK1,transcriptome 02 |
| GSM4009061 |
LLC-PK1,transcriptome 03 |
| GSM4009062 |
HPTC-05-LTR,transcriptome 01 |
| GSM4009063 |
HPTC-05-LTR,transcriptome 02 |
| GSM4009064 |
HPTC-05-LTR,transcriptome 03 |
| GSM4009065 |
HPTC-05-CLA,transcriptome 01 |
| GSM4009066 |
HPTC-05-CLA,transcriptome 02 |
| GSM4009067 |
HKC8,transcriptome 01 |
| GSM4009068 |
HKC8,transcriptome 02 |
| GSM4009069 |
HK2,transcriptome 02 |
| GSM4009070 |
HKC11,transcriptome 01 |
| GSM4009071 |
HKC11,transcriptome 02 |
| GSM4009072 |
HKC11,transcriptome 03 |
| GSM4009073 |
HK2,transcriptome 01 |
| GSM4009074 |
C57BL6/J,transcriptome 03 |
| GSM4009075 |
C57BL6/J,transcriptome 01 |
| GSM4009076 |
C57BL6/J,transcriptome 02 |
| GSM4009077 |
HKC8,transcriptome 03 |
| GSM4249046 |
Primary mPT,transcriptome 01 |
| GSM4249048 |
Primary mPT,transcriptome 02 |
| GSM4249049 |
OK-WT,transcriptome 02 |
| GSM4249050 |
OK-WT,transcriptome 03 |
| GSM4249051 |
OK-WT,transcriptome 04 |
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| Relations |
| BioProject |
PRJNA558898 |
| SRA |
SRP217532 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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