National Heart, Lung, and Blood Institute Epithelial Systems Biology Laboratory

RNA-seq Analysis of Microdissected Rat Kidney Tubule Segments

This database provides median RPKM values for the transcriptome of 14 separate renal tubule segments in untreated male Sprague-Dawley rats (200-250 g BW). The number of replicates is shown in parentheses.

Brief Method: Rat renal tubule segments manually dissected under microscope were lysed in cell lysis buffer containing reverse transcriptase and oligo-dT primers. After reverse transcription of poly(A)-tailed mRNA transcripts, cDNAs were amplified and sequenced using Illumina HiSeq 2000 sequencer. FASTQ sequences were mapped to rat reference genome (rn5).

How to search the database: Please use the Search Box at the right upper corner of the table.

Terminology for nephron segments: S1, first segment of the proximal tubule; S2, second segment of the proximal tubule; S3, third segment of the proximal tubule; SDL, short descending limb of the loop of Henle; LDLOM, long descending limb of the loop of Henle in the outer medulla; LDLIM, long descending limb of the loop of Henle in the inner medulla; tAL, thin ascending limb of the loop of Henle; mTAL, medullary thick ascending limb of the loop of Henle; cTAL, cortical thick ascending limb of the loop of Henle; DCT, distal convoluted tubule; CNT, connecting tubule; CCD, cortical collecting duct; OMCD, outer medullary collecting duct; IMCD, inner medullary collecting duct

Reference: Lee JW, Chou CL, and Knepper MA. Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes. J Am Soc Nephrol 2015 Mar 27. pii: ASN.2014111067 PMID: 25817355

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Gene RefSeq ID S1 (7) S2 (7) S3 (7) SDL (10) LDLOM (9) LDLIM (4) tAL (7) mTAL (7) cTAL (7) DCT (9) CNT (6) CCD (11) OMCD (7) IMCD (8)