GEO DataSets

(Submitter supplied) 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. more...

Organism:

Didelphis virginiana; Sus scrofa; Mus musculus; Canis lupus familiaris; Rattus norvegicus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

6 related Platforms

43 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

125 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Purpose: We used RNA-seq to determine the mRNA species and cell types presented in the whole kidney tissue. Methods: We extracted RNA from the whole kidney tissue and microdissected proximal tubules. cDNA libraries were constructed for paired-end sequencing and sequenced on Illumina HiSeq3000 platform.Reads were mapped to mouse Ensembl Genome by STAR and transcript abundances were calculated in the units of transcripts per million (TPM) using RSEM (https://github.com/deweylab/RSEM). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

15 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

28 Samples

Download data: BW

(Submitter supplied) We performed CUT&RUN sequencing to characterize HNF4A binding sites in human adult kidney and kidney organoid-derived proximal tubular cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) We performed bulk RNA-seq and compared complehensive gene expression profiles of kidney organoids induced from wild type, HNF4A-KO, HNF4G-KO, and HNF4A/4G-DKO iPS cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: TSV

(Submitter supplied) The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney, the pronephros, represents a simplified form of the mammalian organ, yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: CSV

(Submitter supplied) Characterization of gene expression for each renal cell type is essential for identifying mechanisms underlying kidney physiology and pathophysiology. Here, we built a transcriptome landscape mouse renal epithelial cells by deep sequencing of all 14 mouse renal segments, upon which we developed an enrichment protocol to characterize distal nephron cells by single-cell RNA-seq. Our renal tubule expression atlas provided landscapes of gene expression and alternative splicing along the renal tubule segments. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

96 Samples

Download data: RDATA, TAR, TXT

(Submitter supplied) The multiligand receptor megalin and its endocytic adaptor protein Dab2 play essential roles in maintaining the integrity of the apical endocytic pathway of proximal tubule cells, and have complex and poorly understood roles in the development of chronic kidney disease. Here we used RNASeq in CRISPR/Cas9 knockout technology in a well-differentiated cell culture model to identify PT-specific transcriptional changes that are directly consequent to the loss of megalin (Lrp2), cubilin (Cubn), or Dab2 (Dab2) expression.

Organism:

Didelphis virginiana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23025

12 Samples

Download data: CSV, XLSX