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Series GSE111837 Query DataSets for GSE111837
Status Public on Jan 17, 2019
Title Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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 (
Results and conclusion: Based on a variety of data types we curated a list of 43 cell types that are thought to exist in the kidney. Our data indicated that, If mRNA levels parallel protein levels, the contribution of proximal tubules to total mRNA in the renal tubule is also likely to be in the vicinity of 66%.
Overall design cDNAs from whole kidney tissue and microdissected proximal tubules were generated and sequenced using Illumina HiSeq 3000.
Contributor(s) Clark JZ, Chen L, Chou C, Jung H, Lee J, Knepper MA
Citation(s) 30826016
Submission date Mar 14, 2018
Last update date Jun 08, 2023
Contact name Lihe Chen
Phone 3015947152
Organization name NHLBI
Street address 10 center drive MSC 1603, Building 10, Room 6N318
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (15)
GSM3040822 Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 01
GSM3040823 Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 02
GSM3040824 Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 03
BioProject PRJNA438336
SRA SRP135698

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Supplementary file Size Download File type/resource
GSE111837_Microdissected_mouse_PTS2.txt.gz 1.7 Mb (ftp)(http) TXT
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Processed data are available on Series record

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