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Series GSE125701 Query DataSets for GSE125701
Status Public on Apr 14, 2020
Title Comparative transcriptome profiling myometrial and vascular smooth muscle cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this study was to select the optimal myometrial cells for our high-throughput drug discovery assay, as well as determine the similarity or differences of myometrial cells to vascular smooth muscle cells (VSMCs)-the most common off-target of current myometrial therapeutics. RNA-seq was used to: 1) identify which myometrial cells retained the most similar transcriptome profile to native tissue, and 2) compare the uterine myometrial transcriptome to VSMCs in hopes of identifying a uterine-selective transcriptome that was “druggable” for tocolytic or uterotonic use. Four sources of myometrial cells were examined: 1) term pregnant human primary myometrial cells isolated from tissue biopsies obtained at the time of caesarean sections, 2) term pregnant mouse primary myometrial cells, 3) commercially-available immortalized pregnant human myometrial (PHM1) cells and 4) human telomerase immortalized myometrial (hTERT-HM) cells. Correlation analysis of aligned reads identified that the transcriptome of primary human myometrial and hTERT-HM cells showed 85% and 80% correlation, respectively, to human myometrial tissue and that the transcriptome of hTERT-HM and PHM1 cells is 90% or more correlative to human primary myometrial cells. The expression levels (fold-change) of contraction-associciated transcripts (OXTR, PTGFR, PTGS2 and GJA1) strongly correlated (r=0.93) between RNA sequencing and qRT-PCR analysis. Analysis of aligned reads among myometrial cells revealed the number of differentially expressed transcripts (fold-change≥2.0, adjusted p-value≤0.01) relative to primary human myometrial cells: hTERT-HM (946 upregulated and 2,351 downregulated), PHM1 (1,575 upregulated and 2,415 downregulated) and primary mouse myometrial cells (3,435 upregulated and 2,966 downregulated). Correlation analysis showed that the human primary myometrial cell transcriptome is over 90% similar to the transcriptome of VSMCs examined. A number of genes associated with smooth muscle contractile machinery (TPM1, TPM2, CNN1, CALD1, ACTA2 and PLN)were significantly (p≤0.01) upregulated (≥2-fold) in human primary myometrial compared to vascular SMCs. We identified 498 transcripts were identified as upregulated in human primary myometrial cells compared to all three VSMCs examined. Of these, the drug-gene interaction database identified 142 genes as druggable
Overall design Myometrial tissue was obtained at the time of scheduled or repeat cesarean section from 5 different women (age 18-45 years) at ≥ 39 gestational weeks . Tissue was used for either RNA isolation for sequencing, or isolation of primary cells. We also isolated primary myometrial cells from 5 different term-pregnant (day 19). PHM1 and adult aorta cells were purchased from ATCC, and fetal aorta cells were purchased from Cell Applications. Immortalized hTERT-HM and fetal DA cells were kindly provided by Drs. Jennifer Condon and Elaine Shelton, respectively. Total RNA was isolated per the Trizol's manufacturer's instructions and then DNase-treated. The RNA was analyzed with an Agilent Bioanalyzer 2100, which showed that all samples had an RIN>8. The coding RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and paired end libraries were generated using the NEBNext Ultra II Directional RNA Library Kit for Illumina (7760). Sequencing was performed at paired-end 100 bp on the Illumina NovaSeq6000 targeting 30M PE reads. Sequencing quality and sample integrity was assessed using the multiQC tools ( as well as positive controls and sample yield. Quantitative RT-PCR validation was performed using SYBR green assays. The drug-gene interaction database was used to identify the number of druggable transcripts that were upregulated in human primary myometrial cells compared to VSMCs.
Contributor(s) Herington JL, Siricilla S, Sheng Q, Reese J, Shelton EL
Citation(s) 31078743
Submission date Jan 26, 2019
Last update date Apr 14, 2020
Contact name Dhivya Sudhan
Organization name Vanderbilt University
Department Hematology/Oncology Division
Street address 777 Preston Research Building
City Nashville
State/province TN
ZIP/Postal code 37232-6307
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (35)
GSM3580599 Human_adult_aorta_cell_3_RNASeq
GSM3580600 Human_adult_aorta_cell_2_RNASeq
GSM3580601 Human_adult_aorta_cell_1_RNASeq
BioProject PRJNA517268
SRA SRP182138

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Supplementary file Size Download File type/resource
GSE125701_20181130_rnaseq_2392_human_mouse.txt.gz 886.7 Kb (ftp)(http) TXT
GSE125701_rnaseq_2392_human.proteincoding.count.txt.gz 1.3 Mb (ftp)(http) TXT
GSE125701_rnaseq_2392_mouse.proteincoding.count.txt.gz 585.3 Kb (ftp)(http) TXT
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