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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
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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 (https://github.com/deweylab/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%.
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Overall design |
cDNAs from whole kidney tissue and microdissected proximal tubules were generated and sequenced using Illumina HiSeq 3000.
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Contributor(s) |
Clark JZ, Chen L, Chou C, Jung H, Lee J, Knepper MA |
Citation(s) |
30826016 |
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http://dx.doi.org/10.1101/348615
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Submission date |
Mar 14, 2018 |
Last update date |
Jun 08, 2023 |
Contact name |
Lihe Chen |
E-mail(s) |
lihe.chen@nih.gov
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Phone |
3015947152
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Organization name |
NHLBI
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Street address |
10 center drive MSC 1603, Building 10, Room 6N318
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City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
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Platforms (1) |
GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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Samples (15)
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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 |
GSM3040825 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 04 |
GSM3040826 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 05 |
GSM3040827 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 06 |
GSM3040828 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 07 |
GSM3040829 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 08 |
GSM3040830 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 09 |
GSM3040831 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 10 |
GSM3040832 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 11 |
GSM3040833 |
Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 12 |
GSM3040834 |
Whole Kidney RNA-Seq, transcriptome 01 |
GSM3040835 |
Whole Kidney RNA-Seq, transcriptome 02 |
GSM3040836 |
Whole Kidney RNA-Seq, transcriptome 03 |
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Relations |
BioProject |
PRJNA438336 |
SRA |
SRP135698 |
Supplementary file |
Size |
Download |
File type/resource |
GSE111837_Microdissected_mouse_PTS2.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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