Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

RNA-seq Analysis of Microdissected Rat Kidney Tubule Segments (RNA-seq Analysis of Microdissected Rat Kidney Tubule Segments)

General information

Description: The main product of this work is an extensive database of gene expression along the nephron provided as publicly accessible. The data also provide genome-wide maps of alternative exon usage and polyadenylation sites in the kidney.
Year founded: 2015
Last update:
Version:
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: National Institutes of Health
Address: Dr. Mark A. Knepper, National Institutes of Health, Building 10, Room 6N307, 10 Center Drive, MSC-1603, Bethesda, MD 20892-1603.
City:
Province/State: Maryland
Country/Region: United States
Contact name (PI/Team): Mark A. Knepper
Contact email (PI/Helpdesk): knep@helix.nih.gov

Record metadata

Created on: 2018-01-28
Curated by:
Lina Ma [2018-04-23]
Sidra Younas [2018-04-13]

Ranking

All databases:
230/4549 (94.966%)
Expression:
29/800 (96.5%)
230
Total Rank
157
Citations
31.4
z-index

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Publications

25817355
Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes. [PMID: 25817355]
Lee JW, Chou CL, Knepper MA.

The function of each renal tubule segment depends on the genes expressed therein. High-throughput methods used for global profiling of gene expression in unique cell types have shown low sensitivity and high false positivity, thereby limiting the usefulness of these methods in transcriptomic research. However, deep sequencing of RNA species (RNA-seq) achieves highly sensitive and quantitative transcriptomic profiling by sequencing RNAs in a massive, parallel manner. Here, we used RNA-seq coupled with classic renal tubule microdissection to comprehensively profile gene expression in each of 14 renal tubule segments from the proximal tubule through the inner medullary collecting duct of rat kidneys. Polyadenylated mRNAs were captured by oligo-dT primers and processed into adapter-ligated cDNA libraries that were sequenced using an Illumina platform. Transcriptomes were identified to a median depth of 8261 genes in microdissected renal tubule samples (105 replicates in total) and glomeruli (5 replicates). Manual microdissection allowed a high degree of sample purity, which was evidenced by the observed distributions of well established cell-specific markers. The main product of this work is an extensive database of gene expression along the nephron provided as a publicly accessible webpage (https://helixweb.nih.gov/ESBL/Database/NephronRNAseq/index.html). The data also provide genome-wide maps of alternative exon usage and polyadenylation sites in the kidney. We illustrate the use of the data by profiling transcription factor expression along the renal tubule and mapping metabolic pathways.

J Am Soc Nephrol. 2015:26(11) | 157 Citations (from Europe PMC, 2020-02-08)