RNA-seq Analysis of Microdissected Mouse Kidney Tubule Segments


A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse.

J Am Soc Nephrol 2021, PMID: 33769951


Brief Method: kidneys from 6-week-old WT male and female mice (only female proximal tubules were included in this database) were perfused via the left ventricle with perfusion buffer (135 mM NaCl, 1 mM Na2HPO4, 1.2 mM Na2SO4, 1.2 mM MgSO4, 5 mM KCl, 2 mM CaCl2, 5.5 mM glucose, 5 mM HEPES, pH 7.4). kidneys were then sliced and dissociated in perfusion buffer supplemented with collagenase B. Microdissection were performed under the stereomicroscope equipped with on-stage cooling. After washes in ice-cold PBS, the microdissected renal tubules were transferred to Trizol reagent for RNA extraction. cDNAs were synthesized by SMARTer V4 kit (Clontech) and 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).

Terminology: PTS1 the initial segment of the proximal convoluted tubule; PTS2 , proximal straight tubule in cortical medullary rays; PTS3 , last segment of the proximal straight tubule in the outer stripe of outer medulla; DTL1 , the short descending limb of the loop of Henle; DTL2 , long descending limb of the loop of Henle in the outer medulla; DTL3 , long descending limb of the loop of Henle in the inner medulla; ATL , 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. Microdissected mouse glomerulus transcriptome data can be accessed at Mouse Glomerulus Atlas .

Contact: This website was created by Lihe Chen and Mark A. Knepper. Please contact: knep@helix.nih.gov .



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View the data in Santa Cruz Genome Browser or IGV below







Gene Group Expression Landscape








Nephron Segment Specific Genes (3709)








Gene Expression in Human Tissues and Mouse Kidney











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Mouse Nephron Gene Expression Mean TPM

Mouse Nephron Gene Expression Replicates TPM

Mouse Nephron Gene Expression Replicates Counts

Mouse Nephron Differential Genes

Contact

Mark A. Knepper, MD, Ph.D.
knep@helix.nih.gov

Lihe Chen, Ph.D.
lihe.chen@nih.gov
image/svg+xml IMCD OMCD CCD CNT DCT CTAL MTAL ATL DTL3 DTL2 DTL1 PTS3 PTS2 PTS1 outlineC outlineB outlineA Cortex Outer Stripe Inner Stripe InnerMedulla OuterMedulla 1 1 2 2 3 3 4 4 5 6 6 7 7 8 8 9* 9 10 11 12 1. Glomerulus: podocyte (PODO), parietal epithelial cell,mesangial cell, glomerular endothelial cell 2. Proximal convoluted tubule (PCT cell) 3. Proximal straight tubule (PST cell) 4. Thin descending limb of Henle's loop (DTL1,DTL2,and DTL3 cells) 5. Thin ascending limb of Henle's loop (ATL cell) 7. Macula densa (MD) cell (very low abundance in whole kidney) 6. Thick ascending limb (TAL) of Henle's loop: medullary (MTAL cell)and cortical (CTAL cell) 8. Distal convoluted tubule (DCT) cell (divided into DCT1 and DCT2 cells in some species) 9. Connecting tubule (CNT) cell, type B intercalated cell (B-IC), andnon-A, non-B intercalated cell 10. Cortical collecting duct: pricipal cell (PC), type A intercalated cell (A-IC), and type B intercalated cell (B-IC) 11. Outer medullary collecting duct: principal cell (PC) and type A intercalated cell (A-IC) 12. Inner medullary collecting duct: IMCD cell