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).
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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
|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)|