hescs samples gene expression data Search Results


endometrial stromal fibroblasts  (ATCC)
96
ATCC endometrial stromal fibroblasts
( A ) Ancestral construction of HTR2B expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that HTR2B is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface, decidual stromal cell (DSC) clusters are labeled and highlighted (left). Feature plot based on the UMAP plot showing the single-cell expression of HTR2B in the <t>endometrial</t> stromal lineage cells. ( C ) Average expression of HTR2B in RNA-Seq data from human, rat, mouse, rabbit, cow, mink, and opossum endometrial stromal <t>fibroblasts</t> (ESFs). Data are shown as square root (SQRT) transformed transcripts per million (TPM), n = 2. ( D ) Pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of DSCs and perivascular trajectories using the top 2000 differentially expressed genes projected into a two-dimensional space. HTR2B , IL15 , INSR , PRDM1 , REN , and RGS5 expression (log-transformed counts) in individual cells are shown in red along the pseudotime trajectory. IL15 , INSR , and PRDM1 mark DSCs, REN and RGS5 mark perivascular and decidualizing ESFs (dESFs). ( E ) Volcano plot showing genes that are differentially expressed between HTR2B + and HTRB − decidual stromal cells. Horizontal dashed line indicates −Log 10 + = 2 (FDR corrected two-way Fisher’s exact test). ( F ) Word Cloud showing enriched pathways (pink) and disease ontologies (green) in which genes that are differentially expressed between HTR2B + and HTR2B − cells are enriched. Figure 5—source data 1. Genes that are differentially expressed between HTR2B + and HTR2B − cells, and the pathways/disease ontologies in which they are enriched.
Endometrial Stromal Fibroblasts, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/hescs+samples+gene+expression+data/pmc08660021-272-2-7?v=ATCC
Average 96 stars, based on 1 article reviews
endometrial stromal fibroblasts - by Bioz Stars, 2026-07
96/100 stars
  Buy from Supplier

Image Search Results


( A ) Ancestral construction of HTR2B expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that HTR2B is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface, decidual stromal cell (DSC) clusters are labeled and highlighted (left). Feature plot based on the UMAP plot showing the single-cell expression of HTR2B in the endometrial stromal lineage cells. ( C ) Average expression of HTR2B in RNA-Seq data from human, rat, mouse, rabbit, cow, mink, and opossum endometrial stromal fibroblasts (ESFs). Data are shown as square root (SQRT) transformed transcripts per million (TPM), n = 2. ( D ) Pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of DSCs and perivascular trajectories using the top 2000 differentially expressed genes projected into a two-dimensional space. HTR2B , IL15 , INSR , PRDM1 , REN , and RGS5 expression (log-transformed counts) in individual cells are shown in red along the pseudotime trajectory. IL15 , INSR , and PRDM1 mark DSCs, REN and RGS5 mark perivascular and decidualizing ESFs (dESFs). ( E ) Volcano plot showing genes that are differentially expressed between HTR2B + and HTRB − decidual stromal cells. Horizontal dashed line indicates −Log 10 + = 2 (FDR corrected two-way Fisher’s exact test). ( F ) Word Cloud showing enriched pathways (pink) and disease ontologies (green) in which genes that are differentially expressed between HTR2B + and HTR2B − cells are enriched. Figure 5—source data 1. Genes that are differentially expressed between HTR2B + and HTR2B − cells, and the pathways/disease ontologies in which they are enriched.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) Ancestral construction of HTR2B expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that HTR2B is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface, decidual stromal cell (DSC) clusters are labeled and highlighted (left). Feature plot based on the UMAP plot showing the single-cell expression of HTR2B in the endometrial stromal lineage cells. ( C ) Average expression of HTR2B in RNA-Seq data from human, rat, mouse, rabbit, cow, mink, and opossum endometrial stromal fibroblasts (ESFs). Data are shown as square root (SQRT) transformed transcripts per million (TPM), n = 2. ( D ) Pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of DSCs and perivascular trajectories using the top 2000 differentially expressed genes projected into a two-dimensional space. HTR2B , IL15 , INSR , PRDM1 , REN , and RGS5 expression (log-transformed counts) in individual cells are shown in red along the pseudotime trajectory. IL15 , INSR , and PRDM1 mark DSCs, REN and RGS5 mark perivascular and decidualizing ESFs (dESFs). ( E ) Volcano plot showing genes that are differentially expressed between HTR2B + and HTRB − decidual stromal cells. Horizontal dashed line indicates −Log 10 + = 2 (FDR corrected two-way Fisher’s exact test). ( F ) Word Cloud showing enriched pathways (pink) and disease ontologies (green) in which genes that are differentially expressed between HTR2B + and HTR2B − cells are enriched. Figure 5—source data 1. Genes that are differentially expressed between HTR2B + and HTR2B − cells, and the pathways/disease ontologies in which they are enriched.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing, Labeling, RNA Sequencing, Transformation Assay

( A ) Temporal dynamics of human endometrium in vivo. Single-cell profiling of the human endometrium in nonpregnant proliferative and secretory phase biopsies ( n = 15). Data available on https://www.reproductivecellatlas.org/ . ( B ) Single-cell analysis of peri-implantation endometrium. Freshly isolated endometrial cells (Luteinizing Hormone (LH) +8; n = 3, LH +10; n = 3) were subjected to scRNA-Seq. t -Distributed stochastic neighbour embedding ( t -SNE) analysis assigned 2847 cells to 5 clusters (four shown). Clusters designated based on canonical marker genes. Data from . ( C ) Deconvolution of in vitro cell types from endometrium. Total RNA isolated from six different in vitro cell types subjected to RNA-Seq analysis from three midluteal biopsies. Endometrial mesenchymal stem cell (eMSC) – colony-forming W5C5+ cells, perivascular cell (PVC) – noncolony-forming W5C5+ cells, transit amplifying cell (TA) – colony-forming W5C5− cells, stromal – noncolony-forming W5C5− cells, epithelial – uterine gland organoids, and uterine natural killer cell (uNK) – CD56-positive cells. Data from . ( D ) Endometrium throughout the menstrual cycle. Publicly available dataset from Gene Expression Omnibus (GEO profiles). Analysis of normal endometrium in distinct phases of the menstrual cycle using Affymetrix Human Genome U133 Plus 2.0 Array (GDS2052). ( E ) Single-cell analysis of the decidual pathway in vitro. Primary endometrial stromal fibroblasts (ESFs) were decidualized in decidual stromal cells (DSCs) with medroxyprogesterone 17-acetate (MPA) and cyclic adenosine monophosphate (cAMP) for 8 days. Cells were collected every 48 hr and subjected to single-cell analysis. Four thousand five hundred and eighty cells were assigned to seven transcriptional states (six shown). Results are presented as transcripts per million (TPM). Data from .

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) Temporal dynamics of human endometrium in vivo. Single-cell profiling of the human endometrium in nonpregnant proliferative and secretory phase biopsies ( n = 15). Data available on https://www.reproductivecellatlas.org/ . ( B ) Single-cell analysis of peri-implantation endometrium. Freshly isolated endometrial cells (Luteinizing Hormone (LH) +8; n = 3, LH +10; n = 3) were subjected to scRNA-Seq. t -Distributed stochastic neighbour embedding ( t -SNE) analysis assigned 2847 cells to 5 clusters (four shown). Clusters designated based on canonical marker genes. Data from . ( C ) Deconvolution of in vitro cell types from endometrium. Total RNA isolated from six different in vitro cell types subjected to RNA-Seq analysis from three midluteal biopsies. Endometrial mesenchymal stem cell (eMSC) – colony-forming W5C5+ cells, perivascular cell (PVC) – noncolony-forming W5C5+ cells, transit amplifying cell (TA) – colony-forming W5C5− cells, stromal – noncolony-forming W5C5− cells, epithelial – uterine gland organoids, and uterine natural killer cell (uNK) – CD56-positive cells. Data from . ( D ) Endometrium throughout the menstrual cycle. Publicly available dataset from Gene Expression Omnibus (GEO profiles). Analysis of normal endometrium in distinct phases of the menstrual cycle using Affymetrix Human Genome U133 Plus 2.0 Array (GDS2052). ( E ) Single-cell analysis of the decidual pathway in vitro. Primary endometrial stromal fibroblasts (ESFs) were decidualized in decidual stromal cells (DSCs) with medroxyprogesterone 17-acetate (MPA) and cyclic adenosine monophosphate (cAMP) for 8 days. Cells were collected every 48 hr and subjected to single-cell analysis. Four thousand five hundred and eighty cells were assigned to seven transcriptional states (six shown). Results are presented as transcripts per million (TPM). Data from .

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: In Vivo, Single-cell Analysis, Isolation, Marker, In Vitro, RNA Sequencing, Gene Expression

( A ) HTR2B is the only serotonin (5-HT) receptor robustly expressed in human ESFs and DSCs. Expression of serotonin receptors in bulk RNA-Seq data (n = 2) from human endometrial stromal fibroblasts (ESF) and ESFs induced into decidual stromal cells (DSC) by cAMP/progesterone treatment for 48 hours. ( B ) Expression of HTR2B in GTEx tissues. Violin plots are colored by anatomical system; the uterus is indicated by an arrow.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) HTR2B is the only serotonin (5-HT) receptor robustly expressed in human ESFs and DSCs. Expression of serotonin receptors in bulk RNA-Seq data (n = 2) from human endometrial stromal fibroblasts (ESF) and ESFs induced into decidual stromal cells (DSC) by cAMP/progesterone treatment for 48 hours. ( B ) Expression of HTR2B in GTEx tissues. Violin plots are colored by anatomical system; the uterus is indicated by an arrow.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing, RNA Sequencing

( A ) HTR2B expression in human endometrial stromal fibroblasts (ESFs) is downregulated by cyclic adenosine monophosphate (cAMP)/progesterone treatment for 48 hr (decidualization into decidual stromal cells [DSCs]). Transcript abundance in RNA-Seq data is shown as transcripts per million (TPM). ( B ) Regulatory elements in human DSCs at the HTR2B locus. ChIP-Seq peaks shown for H3K4me3, H3K27ac, polymerase II (POLII), progesterone receptor (PGR) and the PGR-A isoform, FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI- and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the HTR2B promoter to other locations in the genome shown in gray. ( C ) HTR2B expression is downregulated by in vitro decidualization of ESFs into DSC by cAMP/progesterone treatment, and upregulated by small interfering RNA (siRNA)-mediated knockdown of PGR, GATA2, and FOXO1, but not NR2F2. n = 3 per transcription factor knockdown. ( D ) Relative expression of HTR2B in the proliferative ( n = 6), early ( n = 4), middle ( n = 9), and late ( n = 8) secretory phases of the menstrual cycle. Note that outliers are excluded from the figure but not the regression; 95% CI is shown in gray. Gene expression data from . ( E ) Relative expression of HTR2B in the basal plate from midgestation to term (14–40 weeks, n = 36); 95% confidence interval (CI) is shown in gray. Inset, percent of up- and downregulated genes between weeks 14–19 and 37–40 of pregnancy (false discovery rate [FDR] ≤0.10). Gene expression data from . ( F ) Cumming estimation plot showing mean difference in luminescence for the serotonin dose response. Upper axis shows relative luminescence of human decidual stromal cells (hDSCs) transiently transfected with a luciferase expression vector that drives the transcription of the luciferase reporter gene from a cAMP/PKA response element (pGL4.29[luc2P/CRE/Hygro]) 6 hr after treatment with serotonin (50, 200, and 1000 μM) or vehicle control (water). Lower axes, mean differences are plotted as bootstrap sampling distributions ( n = 5000; the confidence interval is bias-corrected and accelerated). Each mean difference is depicted as a dot. Each 95 % confidence interval is indicated by the vertical error bars. p values indicate the likelihoods of observing the effect sizes, if the null hypothesis of zero difference is true.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) HTR2B expression in human endometrial stromal fibroblasts (ESFs) is downregulated by cyclic adenosine monophosphate (cAMP)/progesterone treatment for 48 hr (decidualization into decidual stromal cells [DSCs]). Transcript abundance in RNA-Seq data is shown as transcripts per million (TPM). ( B ) Regulatory elements in human DSCs at the HTR2B locus. ChIP-Seq peaks shown for H3K4me3, H3K27ac, polymerase II (POLII), progesterone receptor (PGR) and the PGR-A isoform, FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI- and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the HTR2B promoter to other locations in the genome shown in gray. ( C ) HTR2B expression is downregulated by in vitro decidualization of ESFs into DSC by cAMP/progesterone treatment, and upregulated by small interfering RNA (siRNA)-mediated knockdown of PGR, GATA2, and FOXO1, but not NR2F2. n = 3 per transcription factor knockdown. ( D ) Relative expression of HTR2B in the proliferative ( n = 6), early ( n = 4), middle ( n = 9), and late ( n = 8) secretory phases of the menstrual cycle. Note that outliers are excluded from the figure but not the regression; 95% CI is shown in gray. Gene expression data from . ( E ) Relative expression of HTR2B in the basal plate from midgestation to term (14–40 weeks, n = 36); 95% confidence interval (CI) is shown in gray. Inset, percent of up- and downregulated genes between weeks 14–19 and 37–40 of pregnancy (false discovery rate [FDR] ≤0.10). Gene expression data from . ( F ) Cumming estimation plot showing mean difference in luminescence for the serotonin dose response. Upper axis shows relative luminescence of human decidual stromal cells (hDSCs) transiently transfected with a luciferase expression vector that drives the transcription of the luciferase reporter gene from a cAMP/PKA response element (pGL4.29[luc2P/CRE/Hygro]) 6 hr after treatment with serotonin (50, 200, and 1000 μM) or vehicle control (water). Lower axes, mean differences are plotted as bootstrap sampling distributions ( n = 5000; the confidence interval is bias-corrected and accelerated). Each mean difference is depicted as a dot. Each 95 % confidence interval is indicated by the vertical error bars. p values indicate the likelihoods of observing the effect sizes, if the null hypothesis of zero difference is true.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing, RNA Sequencing, ChIP-sequencing, HiChIP, In Vitro, Small Interfering RNA, Knockdown, Gene Expression, Transfection, Luciferase, Plasmid Preparation, Control, Sampling

( A ) Schematic of the luciferase-based pathway reporter system. Pathways leading to luciferase expression from the cAMP/PKA (pGL4.29[luc2P/CRE/Hygro]), AP1 (pGL4.44[luc2P/AP1-RE/Hygro]), MAPK/ERK (pGL4.33[luc2P/SRE/Hygro]), and Serum Response Factor Response Element (pGL4.34[luc2P/SRF-RE/Hygro]) reporter vectors upon serotonin treatment are shown. ( B ) Cumming estimation plots showing mean difference in luminescence for the serotonin dose response from pathway reporter vectors. Upper plots show relative luminescence of human endometrial stromal fibroblasts (ESFs; ND for nondecidualized) or decidual stromal cells (DSCs; D for decidualized) transiently transfected with a luciferase expression vector that drives the transcription of the indicated luciferase reporter gene 6 hr after treatment with serotonin (50, 200, and 1000 μM) or vehicle control (0). Lower plots, mean differences are plotted as bootstrap sampling distributions ( n = 5000; the confidence interval is bias-corrected and accelerated). Each mean difference is depicted as a dot. Each 95 % confidence interval is indicated by the vertical error bars. p values indicate the likelihoods of observing the effect sizes, if the null hypothesis of zero difference is true. AP1 ESF results. The unpaired mean difference between AP1_ND_0 and AP1_ND_50 is −1.26 [95.0% confidence interval, CI −5.14, 1.77]. The p value of the two-sided permutation t -test is 0.652. The unpaired mean difference between AP1_ND_0 and AP1_ND_200 is 2.28 [95.0% CI −1.93, 4.54]. The p value of the two-sided permutation t -test is 0.292. The unpaired mean difference between AP1_ND_0 and AP1_ND_1000 is 0.684 [95.0% CI −3.99, 3.44]. The p value of the two-sided permutation t -test is 0.693. AP1 DSC results. The unpaired mean difference between AP1_D_0 and AP1_D_50 is 3.45 [95.0% CI −2.37, 9.23]. The p value of the two-sided permutation t -test is 0.31. The unpaired mean difference between AP1_D_0 and AP1_D_200 is −3.72 [95.0% CI −10.1, 1.14]. The p value of the two-sided permutation t -test is 0.392. The unpaired mean difference between AP1_D_0 and AP1_D_1000 is 1.56 [95.0% CI −4.41, 6.91]. The p value of the two-sided permutation t -test is 0.528. Serum response element (SRE) ESF results. The unpaired mean difference between SRE_ND_0 and SRE_ND_50 is 0.74 [95.0% CI −0.361, 2.39]. The p value of the two-sided permutation t -test is 0.494. The unpaired mean difference between SRE_ND_0 and SRE_ND_200 is −0.248 [95.0% CI −0.816, 0.0713]. The p value of the two-sided permutation t -test is 0.403. The unpaired mean difference between SRE_ND_0 and SRE_ND_1000 is 0.164 [95.0% CI −0.361, 0.459]. The p value of the two-sided permutation t -test is 0.405. SRE DSC results. The unpaired mean difference between SRE_D_0 and SRE_D_50 is −0.147 [95.0% CI −0.44, 0.293]. The p value of the two-sided permutation t -test is 0.501. The unpaired mean difference between SRE_D_0 and SRE_D_200 is −0.0399 [95.0% CI −0.336, 0.412]. The p value of the two-sided permutation t -test is 0.793. The unpaired mean difference between SRE_D_0 and SRE_D_1000 is 1.35 [95.0% CI 0.624, 2.69]. The p value of the two-sided permutation t -test is 0.0. SRF ESF results. The unpaired mean difference between SRF_ND_0 and SRF_ND_50 is 0.0203 [95.0% CI −0.101, 0.122]. The p value of the two-sided permutation t -test is 0.516. The unpaired mean difference between SRF_ND_0 and SRF_ND_200 is 0.00516 [95.0% CI −0.114, 0.124]. The p value of the two-sided permutation t -test is 0.727. The unpaired mean difference between SRF_ND_0 and SRF_ND_1000 is −0.0387 [95.0% CI −0.16, 0.0276]. The p value of the two-sided permutation t -test is 0.693. SRF DSC results. The unpaired mean difference between SRF_D_0 and SRF_D_50 is −0.473 [95.0% CI −1.15, −0.0678]. The p value of the two-sided permutation t -test is 0.2. The unpaired mean difference between SRF_D_0 and SRF_D_200 is −0.523 [95.0% CI −1.19, −0.122]. The p value of the two-sided permutation t -test is 0.104. The unpaired mean difference between SRF_D_0 and SRF_D_1000 is −0.511 [95.0% CI −1.22, −0.0742]. The p value of the two-sided permutation t -test is 0.199. CRE ESF results. The unpaired mean difference between CRE_ND_0 and CRE_ND_50 is 0.00845 [95.0% CI −0.255, 0.39]. The p value of the two-sided permutation t -test is 0.798. The unpaired mean difference between CRE_ND_0 and CRE_ND_200 is −0.096 [95.0% CI −0.31, 0.135]. The p value of the two-sided permutation t -test is 0.41. The unpaired mean difference between CRE_ND_0 and CRE_ND_1000 is 0.296 [95.0% CI 0.161, 0.43]. The p value of the two-sided permutation t -test is 0.0. CRE DSC results. The unpaired mean difference between CRE_D_0 and CRE_D_50 is −37.8 [95.0% CI −53.7, −24.1]. The p value of the two-sided permutation t -test is 0.0. The unpaired mean difference between CRE_D_0 and CRE_D_200 is 1.15e+02 [95.0% CI 74.2, 1.39e+02]. The p value of the two-sided permutation t -test is 0.0. The unpaired mean difference between CRE_D_0 and CRE_D_1000 is 1.02e+02 [95.0% CI 77.3, 1.26e+02]. The p value of the two-sided permutation t -test is 0.0.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) Schematic of the luciferase-based pathway reporter system. Pathways leading to luciferase expression from the cAMP/PKA (pGL4.29[luc2P/CRE/Hygro]), AP1 (pGL4.44[luc2P/AP1-RE/Hygro]), MAPK/ERK (pGL4.33[luc2P/SRE/Hygro]), and Serum Response Factor Response Element (pGL4.34[luc2P/SRF-RE/Hygro]) reporter vectors upon serotonin treatment are shown. ( B ) Cumming estimation plots showing mean difference in luminescence for the serotonin dose response from pathway reporter vectors. Upper plots show relative luminescence of human endometrial stromal fibroblasts (ESFs; ND for nondecidualized) or decidual stromal cells (DSCs; D for decidualized) transiently transfected with a luciferase expression vector that drives the transcription of the indicated luciferase reporter gene 6 hr after treatment with serotonin (50, 200, and 1000 μM) or vehicle control (0). Lower plots, mean differences are plotted as bootstrap sampling distributions ( n = 5000; the confidence interval is bias-corrected and accelerated). Each mean difference is depicted as a dot. Each 95 % confidence interval is indicated by the vertical error bars. p values indicate the likelihoods of observing the effect sizes, if the null hypothesis of zero difference is true. AP1 ESF results. The unpaired mean difference between AP1_ND_0 and AP1_ND_50 is −1.26 [95.0% confidence interval, CI −5.14, 1.77]. The p value of the two-sided permutation t -test is 0.652. The unpaired mean difference between AP1_ND_0 and AP1_ND_200 is 2.28 [95.0% CI −1.93, 4.54]. The p value of the two-sided permutation t -test is 0.292. The unpaired mean difference between AP1_ND_0 and AP1_ND_1000 is 0.684 [95.0% CI −3.99, 3.44]. The p value of the two-sided permutation t -test is 0.693. AP1 DSC results. The unpaired mean difference between AP1_D_0 and AP1_D_50 is 3.45 [95.0% CI −2.37, 9.23]. The p value of the two-sided permutation t -test is 0.31. The unpaired mean difference between AP1_D_0 and AP1_D_200 is −3.72 [95.0% CI −10.1, 1.14]. The p value of the two-sided permutation t -test is 0.392. The unpaired mean difference between AP1_D_0 and AP1_D_1000 is 1.56 [95.0% CI −4.41, 6.91]. The p value of the two-sided permutation t -test is 0.528. Serum response element (SRE) ESF results. The unpaired mean difference between SRE_ND_0 and SRE_ND_50 is 0.74 [95.0% CI −0.361, 2.39]. The p value of the two-sided permutation t -test is 0.494. The unpaired mean difference between SRE_ND_0 and SRE_ND_200 is −0.248 [95.0% CI −0.816, 0.0713]. The p value of the two-sided permutation t -test is 0.403. The unpaired mean difference between SRE_ND_0 and SRE_ND_1000 is 0.164 [95.0% CI −0.361, 0.459]. The p value of the two-sided permutation t -test is 0.405. SRE DSC results. The unpaired mean difference between SRE_D_0 and SRE_D_50 is −0.147 [95.0% CI −0.44, 0.293]. The p value of the two-sided permutation t -test is 0.501. The unpaired mean difference between SRE_D_0 and SRE_D_200 is −0.0399 [95.0% CI −0.336, 0.412]. The p value of the two-sided permutation t -test is 0.793. The unpaired mean difference between SRE_D_0 and SRE_D_1000 is 1.35 [95.0% CI 0.624, 2.69]. The p value of the two-sided permutation t -test is 0.0. SRF ESF results. The unpaired mean difference between SRF_ND_0 and SRF_ND_50 is 0.0203 [95.0% CI −0.101, 0.122]. The p value of the two-sided permutation t -test is 0.516. The unpaired mean difference between SRF_ND_0 and SRF_ND_200 is 0.00516 [95.0% CI −0.114, 0.124]. The p value of the two-sided permutation t -test is 0.727. The unpaired mean difference between SRF_ND_0 and SRF_ND_1000 is −0.0387 [95.0% CI −0.16, 0.0276]. The p value of the two-sided permutation t -test is 0.693. SRF DSC results. The unpaired mean difference between SRF_D_0 and SRF_D_50 is −0.473 [95.0% CI −1.15, −0.0678]. The p value of the two-sided permutation t -test is 0.2. The unpaired mean difference between SRF_D_0 and SRF_D_200 is −0.523 [95.0% CI −1.19, −0.122]. The p value of the two-sided permutation t -test is 0.104. The unpaired mean difference between SRF_D_0 and SRF_D_1000 is −0.511 [95.0% CI −1.22, −0.0742]. The p value of the two-sided permutation t -test is 0.199. CRE ESF results. The unpaired mean difference between CRE_ND_0 and CRE_ND_50 is 0.00845 [95.0% CI −0.255, 0.39]. The p value of the two-sided permutation t -test is 0.798. The unpaired mean difference between CRE_ND_0 and CRE_ND_200 is −0.096 [95.0% CI −0.31, 0.135]. The p value of the two-sided permutation t -test is 0.41. The unpaired mean difference between CRE_ND_0 and CRE_ND_1000 is 0.296 [95.0% CI 0.161, 0.43]. The p value of the two-sided permutation t -test is 0.0. CRE DSC results. The unpaired mean difference between CRE_D_0 and CRE_D_50 is −37.8 [95.0% CI −53.7, −24.1]. The p value of the two-sided permutation t -test is 0.0. The unpaired mean difference between CRE_D_0 and CRE_D_200 is 1.15e+02 [95.0% CI 74.2, 1.39e+02]. The p value of the two-sided permutation t -test is 0.0. The unpaired mean difference between CRE_D_0 and CRE_D_1000 is 1.02e+02 [95.0% CI 77.3, 1.26e+02]. The p value of the two-sided permutation t -test is 0.0.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Luciferase, Expressing, Transfection, Plasmid Preparation, Control, Sampling

( A ) Ancestral construction of PDCD1LG2 expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that PDCD1LG2 is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface. PDCD1LG2 expression (log-transformed counts) in individual cells is shown in red. ( C ) Left: proportion of cell types at the maternal–fetal interface that express PDCD1LG2 . Only cell types that express PDCD1LG2 are shown as a 100 % stacked bar chart: decidual stromal cell populations 1–3 (DSC1–3), average expression in DSC1–3, dendritic cells (DCs), macrophage (MP), and extravillus cytotrophoblasts (evCTB). Right: pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of DSCs and perivascular trajectories projected into a two-dimensional space. PDCD1LG2 expression (log-transformed counts) in individual cells is shown in red along the pseudotime trajectory. ( D ) Average expression of PDCD1LG2 in RNA-Seq data from human, rat, mouse, rabbit, cow, mink, and opossum endometrial stromal fibroblasts (ESFs). Data are shown as square root (SQRT) transformed transcripts per million (TPM), n = 2. ( E ) Regulatory elements in human DSCs at the PDCD1LG2 locus. ChIP-Seq peaks shown for H3K4me1, H3K4me3, H3K27ac, polymerase II (POLII), progesterone receptor (PGR), FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI-, ATAC-, and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the PDCD1LG2 promoter to other locations in the genome shown in gray. The location of SNPs implicated by genome-wide association study (GWAS) in preterm birth is shown in red. ( F ) PDCD1LG2 expression in human ESFs is downregulated by cyclic adenosine monophosphate (cAMP)/progesterone treatment for 48 hr (decidualization into DSCs). Transcript abundance in RNA-Seq data is shown as TPM. ( G ) PDCD1LG2 expression is downregulated by in vitro decidualization of ESFs into DSC by cAMP/progesterone treatment and by siRNA-mediated knockdown of FOXO1. siRNA-mediated knockdown of PGR upregulated PDCD1LG2 expression, while there was no effect after siRNA-mediated knockdown of NR2F2 or GATA2. n = 3 per transcription factor knockdown.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) Ancestral construction of PDCD1LG2 expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that PDCD1LG2 is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface. PDCD1LG2 expression (log-transformed counts) in individual cells is shown in red. ( C ) Left: proportion of cell types at the maternal–fetal interface that express PDCD1LG2 . Only cell types that express PDCD1LG2 are shown as a 100 % stacked bar chart: decidual stromal cell populations 1–3 (DSC1–3), average expression in DSC1–3, dendritic cells (DCs), macrophage (MP), and extravillus cytotrophoblasts (evCTB). Right: pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of DSCs and perivascular trajectories projected into a two-dimensional space. PDCD1LG2 expression (log-transformed counts) in individual cells is shown in red along the pseudotime trajectory. ( D ) Average expression of PDCD1LG2 in RNA-Seq data from human, rat, mouse, rabbit, cow, mink, and opossum endometrial stromal fibroblasts (ESFs). Data are shown as square root (SQRT) transformed transcripts per million (TPM), n = 2. ( E ) Regulatory elements in human DSCs at the PDCD1LG2 locus. ChIP-Seq peaks shown for H3K4me1, H3K4me3, H3K27ac, polymerase II (POLII), progesterone receptor (PGR), FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI-, ATAC-, and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the PDCD1LG2 promoter to other locations in the genome shown in gray. The location of SNPs implicated by genome-wide association study (GWAS) in preterm birth is shown in red. ( F ) PDCD1LG2 expression in human ESFs is downregulated by cyclic adenosine monophosphate (cAMP)/progesterone treatment for 48 hr (decidualization into DSCs). Transcript abundance in RNA-Seq data is shown as TPM. ( G ) PDCD1LG2 expression is downregulated by in vitro decidualization of ESFs into DSC by cAMP/progesterone treatment and by siRNA-mediated knockdown of FOXO1. siRNA-mediated knockdown of PGR upregulated PDCD1LG2 expression, while there was no effect after siRNA-mediated knockdown of NR2F2 or GATA2. n = 3 per transcription factor knockdown.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing, Transformation Assay, RNA Sequencing, ChIP-sequencing, HiChIP, GWAS, In Vitro, Knockdown

( A ) Ancestral construction of CORIN expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that CORIN is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface. CORIN expression (log-transformed counts) in individual cells is shown in red. ( C ) Pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of decidual stromal cells (DSCs) and perivascular trajectories projected into a two-dimensional space. CORIN expression (log-transformed counts) in individual cells is shown in red along the pseudotime trajectory. ( D ) CORIN expression in human endometrial stromal fibroblasts (ESFs) is upregulated by cAMP/progesterone treatment for 48 hr (decidualization into DSCs). Transcript abundance in RNA-Seq data is shown as transcripts per million (TPM). ( E ) Regulatory elements in human DSCs at the CORIN locus. ChIP-Seq peaks shown for H3K4me3, polymerase II (POLII), progesterone receptor (PGR), FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI-, ATAC-, and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the CORIN promoter to other locations in the genome shown in gray. ( F ) CORIN expression is upregulated by in vitro decidualization of ESFs into DSC by cyclic adenosine monophosphate (cAMP/progesterone treatment, and down)regulated by siRNA-mediated knockdown of PGR and GATA2, but not FOXO1 or NR2F2. n = 3 per transcription factor knockdown.

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: ( A ) Ancestral construction of CORIN expression in gravid/pregnant endometrium. Pie charts indicate the Bayesian posterior probability (BPP) that CORIN is expressed (state 1) or not expressed (state 0). ( B ) UMAP clustering of cells from the first trimester maternal–fetal interface. CORIN expression (log-transformed counts) in individual cells is shown in red. ( C ) Pseudotime trajectory of endometrial stromal fibroblast lineage cells. Monocle2 visualization of five distinct clusters of decidual stromal cells (DSCs) and perivascular trajectories projected into a two-dimensional space. CORIN expression (log-transformed counts) in individual cells is shown in red along the pseudotime trajectory. ( D ) CORIN expression in human endometrial stromal fibroblasts (ESFs) is upregulated by cAMP/progesterone treatment for 48 hr (decidualization into DSCs). Transcript abundance in RNA-Seq data is shown as transcripts per million (TPM). ( E ) Regulatory elements in human DSCs at the CORIN locus. ChIP-Seq peaks shown for H3K4me3, polymerase II (POLII), progesterone receptor (PGR), FOXO1, FOSL2, GATA2, and NR2F2 (COUP-TFII). Regions of open chromatin are shown from DNaseI-, ATAC-, and FAIRE-Seq. Chromatin loops inferred from H3K27ac HiChIP are shown as black arcs connecting the CORIN promoter to other locations in the genome shown in gray. ( F ) CORIN expression is upregulated by in vitro decidualization of ESFs into DSC by cyclic adenosine monophosphate (cAMP/progesterone treatment, and down)regulated by siRNA-mediated knockdown of PGR and GATA2, but not FOXO1 or NR2F2. n = 3 per transcription factor knockdown.

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing, Transformation Assay, RNA Sequencing, ChIP-sequencing, HiChIP, In Vitro, Knockdown

Expression of placental enriched genes in RNA-Seq data from human placenta, endometrial stromal fibroblasts (ESFs), decidual stromal cells (DSCs), and human first trimester decidua. Expression levels are shown as transcripts per million (TPM) values, the Tissue Specificity (TS) score is calculated as the fold enrichment of each gene relative to the tissue with the second highest expression of that gene. Placental data are from https://www.proteinatlas.org/humanproteome/tissue/placenta .

Journal: eLife

Article Title: Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

doi: 10.7554/eLife.69584

Figure Lengend Snippet: Expression of placental enriched genes in RNA-Seq data from human placenta, endometrial stromal fibroblasts (ESFs), decidual stromal cells (DSCs), and human first trimester decidua. Expression levels are shown as transcripts per million (TPM) values, the Tissue Specificity (TS) score is calculated as the fold enrichment of each gene relative to the tissue with the second highest expression of that gene. Placental data are from https://www.proteinatlas.org/humanproteome/tissue/placenta .

Article Snippet: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (12676029, Thermo Fisher Scientific), 1% L -glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1× insulin–transferrin–selenium (ITS; 41400045, Thermo Fisher Scientific).

Techniques: Expressing