Data from: Role of serotonin in human placental cytotrophoblast differentiation and gene expression
Data files
Jul 30, 2025 version files 250.22 MB
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5HT_vs_Ctrl_DESeq2_fulltable.xlsx
7.61 MB
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5HT_vs_Ctrl_padj0.05_FC1_DEG9.xlsx
8.07 KB
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5HT_vs_Ctrl_padj0.05_FC2_DEG9.xlsx
8.08 KB
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5HT_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
8.20 MB
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5HT_vs_cys_2b_5HT_padj0.05_FC1_DEG2897.xlsx
564.27 KB
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5HT_vs_cys_2b_5HT_padj0.05_FC2_DEG2732.xlsx
530.08 KB
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5HT_vs_cys_DESeq2_fulltable.xlsx
8.18 MB
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5HT_vs_cys_padj0.05_FC1_DEG2949.xlsx
573.20 KB
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5HT_vs_cys_padj0.05_FC2_DEG2787.xlsx
539.64 KB
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5HT_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
7.68 MB
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5HT_vs_lex_2b_5HT_padj0.05_FC1_DEG240.xlsx
52.97 KB
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5HT_vs_lex_2b_5HT_padj0.05_FC2_DEG225.xlsx
49.79 KB
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5HT_vs_lex_DESeq2_fulltable.xlsx
7.40 MB
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5HT_vs_lex_padj0.05_FC1_DEG735.xlsx
140.97 KB
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5HT_vs_lex_padj0.05_FC2_DEG682.xlsx
130.86 KB
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Ctrl_vs_5HT_DESeq2_fulltable.xlsx
7.61 MB
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Ctrl_vs_5HT_padj0.05_FC1_DEG9.xlsx
8.08 KB
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Ctrl_vs_5HT_padj0.05_FC2_DEG9.xlsx
8.08 KB
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Ctrl_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
8.25 MB
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Ctrl_vs_cys_2b_5HT_padj0.05_FC1_DEG2277.xlsx
448.90 KB
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Ctrl_vs_cys_2b_5HT_padj0.05_FC2_DEG2150.xlsx
422.53 KB
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Ctrl_vs_cys_DESeq2_fulltable.xlsx
8.22 MB
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Ctrl_vs_cys_padj0.05_FC1_DEG2293.xlsx
451.41 KB
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Ctrl_vs_cys_padj0.05_FC2_DEG2165.xlsx
424.80 KB
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Ctrl_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
7.62 MB
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Ctrl_vs_lex_2b_5HT_padj0.05_FC1_DEG132.xlsx
31.52 KB
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Ctrl_vs_lex_2b_5HT_padj0.05_FC2_DEG123.xlsx
29.63 KB
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Ctrl_vs_lex_DESeq2_fulltable.xlsx
7.44 MB
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Ctrl_vs_lex_padj0.05_FC1_DEG413.xlsx
82.38 KB
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Ctrl_vs_lex_padj0.05_FC2_DEG396.xlsx
79.14 KB
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cys_2b_5HT_vs_5HT_DESeq2_fulltable.xlsx
8.18 MB
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cys_2b_5HT_vs_5HT_padj0.05_FC1_DEG2897.xlsx
563.60 KB
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cys_2b_5HT_vs_5HT_padj0.05_FC2_DEG2732.xlsx
529.28 KB
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cys_2b_5HT_vs_Ctrl_DESeq2_fulltable.xlsx
8.23 MB
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cys_2b_5HT_vs_Ctrl_padj0.05_FC1_DEG2277.xlsx
448.19 KB
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cys_2b_5HT_vs_Ctrl_padj0.05_FC2_DEG2150.xlsx
421.76 KB
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cys_2b_5HT_vs_cys_DESeq2_fulltable.xlsx
8.17 MB
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cys_2b_5HT_vs_cys_padj0.05_FC1_DEG5.xlsx
7.46 KB
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cys_2b_5HT_vs_cys_padj0.05_FC2_DEG5.xlsx
7.46 KB
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cys_2b_5HT_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
8.15 MB
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cys_2b_5HT_vs_lex_2b_5HT_padj0.05_FC1_DEG1887.xlsx
360.05 KB
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cys_2b_5HT_vs_lex_2b_5HT_padj0.05_FC2_DEG1802.xlsx
342.18 KB
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cys_2b_5HT_vs_lex_DESeq2_fulltable.xlsx
7.80 MB
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cys_2b_5HT_vs_lex_padj0.05_FC1_DEG1942.xlsx
355.25 KB
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cys_2b_5HT_vs_lex_padj0.05_FC2_DEG1839.xlsx
334.98 KB
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cys_vs_5HT_DESeq2_fulltable.xlsx
8.16 MB
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cys_vs_5HT_padj0.05_FC1_DEG2949.xlsx
572.51 KB
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cys_vs_5HT_padj0.05_FC2_DEG2787.xlsx
538.82 KB
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cys_vs_Ctrl_DESeq2_fulltable.xlsx
8.21 MB
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cys_vs_Ctrl_padj0.05_FC1_DEG2293.xlsx
450.78 KB
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cys_vs_Ctrl_padj0.05_FC2_DEG2165.xlsx
424.14 KB
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cys_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
8.18 MB
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cys_vs_cys_2b_5HT_padj0.05_FC1_DEG5.xlsx
7.47 KB
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cys_vs_cys_2b_5HT_padj0.05_FC2_DEG5.xlsx
7.47 KB
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cys_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
8.13 MB
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cys_vs_lex_2b_5HT_padj0.05_FC1_DEG1892.xlsx
359.58 KB
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cys_vs_lex_2b_5HT_padj0.05_FC2_DEG1810.xlsx
342.33 KB
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cys_vs_lex_DESeq2_fulltable.xlsx
7.80 MB
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cys_vs_lex_padj0.05_FC1_DEG1805.xlsx
329.20 KB
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cys_vs_lex_padj0.05_FC2_DEG1715.xlsx
311.68 KB
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lex_2b_5HT_vs_5HT_DESeq2_fulltable.xlsx
7.68 MB
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lex_2b_5HT_vs_5HT_padj0.05_FC1_DEG240.xlsx
52.93 KB
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lex_2b_5HT_vs_5HT_padj0.05_FC2_DEG225.xlsx
49.79 KB
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lex_2b_5HT_vs_Ctrl_DESeq2_fulltable.xlsx
7.62 MB
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lex_2b_5HT_vs_Ctrl_padj0.05_FC1_DEG132.xlsx
31.48 KB
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lex_2b_5HT_vs_Ctrl_padj0.05_FC2_DEG123.xlsx
29.60 KB
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lex_2b_5HT_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
8.16 MB
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lex_2b_5HT_vs_cys_2b_5HT_padj0.05_FC1_DEG1887.xlsx
360.64 KB
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lex_2b_5HT_vs_cys_2b_5HT_padj0.05_FC2_DEG1802.xlsx
342.70 KB
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lex_2b_5HT_vs_cys_DESeq2_fulltable.xlsx
8.14 MB
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lex_2b_5HT_vs_cys_padj0.05_FC1_DEG1892.xlsx
360.05 KB
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lex_2b_5HT_vs_cys_padj0.05_FC2_DEG1810.xlsx
342.82 KB
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lex_2b_5HT_vs_lex_DESeq2_fulltable.xlsx
7.14 MB
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lex_2b_5HT_vs_lex_padj0.05_FC1_DEG18.xlsx
9.49 KB
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lex_2b_5HT_vs_lex_padj0.05_FC2_DEG18.xlsx
9.49 KB
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lex_vs_5HT_DESeq2_fulltable.xlsx
7.39 MB
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lex_vs_5HT_padj0.05_FC1_DEG735.xlsx
141.11 KB
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lex_vs_5HT_padj0.05_FC2_DEG682.xlsx
130.90 KB
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lex_vs_Ctrl_DESeq2_fulltable.xlsx
7.44 MB
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lex_vs_Ctrl_padj0.05_FC1_DEG413.xlsx
82.44 KB
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lex_vs_Ctrl_padj0.05_FC2_DEG396.xlsx
79.25 KB
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lex_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
7.82 MB
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lex_vs_cys_2b_5HT_padj0.05_FC1_DEG1942.xlsx
356.01 KB
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lex_vs_cys_2b_5HT_padj0.05_FC2_DEG1839.xlsx
335.88 KB
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lex_vs_cys_DESeq2_fulltable.xlsx
7.81 MB
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lex_vs_cys_padj0.05_FC1_DEG1805.xlsx
329.93 KB
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lex_vs_cys_padj0.05_FC2_DEG1715.xlsx
312.43 KB
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lex_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
7.13 MB
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lex_vs_lex_2b_5HT_padj0.05_FC1_DEG18.xlsx
9.48 KB
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lex_vs_lex_2b_5HT_padj0.05_FC2_DEG18.xlsx
9.48 KB
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README.md
11.48 KB
Abstract
Serotonin (5-hydroxytryptamine; 5-HT) is transported into the human placenta through the serotonin transporter (SERT/SLC6A4) on the surface of the syncytiotrophoblast, where it ultimately makes its way to the circulation within the conceptus. During this transit a significant amount of 5-HT becomes concentrated in the cytotrophoblast nucleus. We used immunochemistry, inhibitors of SERT and transglutaminase 2 (TGM2; the enzyme that mediates the covalent linkage of 5-HT to protein glutamine residues—a process known as serotonylation), and RNA sequencing to elucidate the mechanism and consequences of this nuclear localization. Exogenous 5-HT recapitulated the uptake of 5-HT into the trophoblasts and its preferential concentration in cytotrophoblast nuclei we observed in the intact placenta. Inhibiting SERT with escitalopram or TGM2 with cystamine blocked cytotrophoblast differentiation in vitro; namely, flattening, aggregation and forming syncytia. Cystamine eliminated the staining of the nuclei in placental explants by exogenous 5-HT, suggesting that serotonylation mediated this phenomenon. This was confirmed by western blots and immunoprecipitation which identified histone 3 (H3), and specifically the 5th glutamine residue in H3, as a site of serotonylation. Blocking serotonylation led to marked changes in RNA expression. Of the 38,524 mRNAs identified in these trophoblasts, cystamine changed the expression of 1,986 and escitalopram significantly altered 374. Both treatments altered the expression of 155 mRNAs either positively or negatively. In general, the genes that were downregulated were involved with cell proliferation, morphogenesis, motility, and growth—while genes that were upregulated controlled cell survival and protection pathways. These findings suggests that maternal 5-HT promotes placental, embryonic/fetal, and organismal development through histone serotonylation and consequent alterations in gene expression. They raise the possibility that alterations in 5-HT flux in the placenta affect placental and fetal growth, as well as organismal somatic and neurologic developmental trajectories.
Dataset DOI: 10.5061/dryad.b8gtht7qb
Description of the data and file structure
This README_Kliman_29Jul2025_Endocrinolgy_DATA.txt file was generated on 6Apr2025, and updated on 29Jul25, by Harvey J. Kliman, MD, PhD
GENERAL INFORMATION
1. Title of Dataset: Endocrinology-S-25-00232 files
2. Author Information
- Harvey J. Kliman, MD, PhD
- Yale University School of Medicine
- harvey.kliman@yale.edu
- Nolwenn S. Morris, PhD
- Yale University School of Medicine
- nolwennsue.morris@yale.edu
3. Date of data collection: 2024
4. Geographic location of data collection: New Haven, CT, USA
5. This work was supported by the Fulbright-Monahan Foundation (NSM), the University of Paris (NSM), and the Reproductive and Placental Research Unit, Yale University School of Medicine (HJK).
6. All the patients who provided term placental samples signed an informed consent (Yale IRB protocol 12696 through the Reproductive Sciences Biobank at Yale University).
7. Please refer to the following citations for methodological details:
1. Kliman HJ, Nestler JE, Sermasi E, Sanger JM, Strauss JF, 3rd. Purification, characterization, and in vitro differentiation of cytotrophoblasts from human term placentae. Endocrinology. 1986;118(4):1567-1582.
2. Tang Z, Tadesse S, Norwitz E, Mor G, Abrahams VM, Guller S. Isolation of hofbauer cells from human term placentas with high yield and purity. Am J Reprod Immunol. 2011;66(4):336-348.
3. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907-915.
4. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290-295.
5. Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, Garcia Giron C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martinez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47(D1):D766-D773.
6. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
7. Zhao Y, Li MC, Konate MM, Chen L, Das B, Karlovich C, Williams PM, Evrard YA, Doroshow JH, McShane LM. TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository. J Transl Med. 2021;19(1):269.
8. Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med. 1990;9(7):811-818.
Files and variables
DATA & FILE OVERVIEW
Number of files: 90
Types of files:
- DESeq2_fulltable (all data with R-based DESeq2 statistical methods to normalize and analyze the RNA-seq data)
- padj0.05_FC1_DEG (Differentially expressed genes with a Log2Fold change >1 or <-1 and a p adjusted value of <0.05)
- padj0.05_FC2_DEG (Differentially expressed genes with a Log2Fold change >2 or <-2 and a p adjusted value of <0.05)
Number of genes/rows:
- DESeq2_fulltable files: always 58,288
- padj0.05_FC1_DEG(n): condition specific; n = number of genes that satisfy these parameters for each condition pair
- padj0.05_FC2_DEG(n): condition specific; n = number of genes that satisfy these parameters for each condition pair
Abbreviations
- 5-HT (serotonin, 5-hydroxytryptamine, CAS 153-98-0)
- Cys (cystamine, CAS 56-17-7)
- Lex (escitalopram oxalate, Lexapro, CAS 219861-08-2)
Variable Lists (Table Column Headers):
- genes: Lists the genes analyzed.
- GeneVer: Version of the gene annotation used.
- GeneID: Unique identifier for each gene.
- GeneType: Type or category of gene (e.g., protein-coding, non-coding.
- GeneName: Standardized name of the gene.
- mean_XXX: Mean of gene expression in XXX condition.
- mean_YYY: Mean of gene expression in YYY condition.
- log2FoldChange: Log2 fold change of expression between the XXX condition and YYY condition.
- lfcSE: Standard error of the log2 fold change.
- stat: Statistical value used to determine significance (e.g., test statistic).
- pvalue: P-value indicating the significance of differential expression.
- padj: Adjusted p-value for multiple testing correction.
- S_12D24_1st condition in file name (12D24 is the experiment designation and hence specific placenta being examined).
- S_21E24_1st condition in file name (21E24 is the experiment designation and hence specific placenta being examined).
- S_27C24_1st condition in file name (27C24 is the experiment designation and hence specific placenta being examined).
- S_12D24_2nd condition in file name (12D24 is the experiment designation and hence specific placenta being examined).
- S_21E24_2nd condition in file name (21E24 is the experiment designation and hence specific placenta being examined).
- S_27C24_2ndcondition in file name (27C24 is the experiment designation and hence specific placenta being examined).
Conditions (stated in file name):
- 5HT_vs_Ctrl: 5-HT v Control
- 5HT_vs_cys_2b_5HT: 5-HT v (Cystamine + 5-HT)
- 5HT_vs_cys: 5-HT v Cystamine
- 5HT_vs_lex_2b_5HT: 5-HT v (escitalopram + 5-HT)
- 5HT_vs_lex: 5-HT v escitalopram
- Ctrl_vs_5HT: Control v 5-HT
- Ctrl_vs_cys_2b_5HT: Control v (Cystamine + 5-HT)
- Ctrl_vs_cys: Control v Cystamine
- Ctrl_vs_lex: 5-HT v escitalopram
- cys_2b_5HT_vs_5HT: (Cystamine + 5-HT) v 5-HT
- cys_2b_5HT_vs_Ctrl: (Cystamine + 5-HT) v Control
- cys_2b_5HT_vs_cys: (Cystamine + 5-HT) v Cystamine
- cys_2b_5HT_vs_lex_2b_5HT: (Cystamine + 5-HT) v (escitalopram + 5-HT)
- cys_2b_5HT_vs_lex: (Cystamine + 5-HT) v escitalopram
- cys_vs_5HT: Cystamine v 5-HT
- cys_vs_Ctrl: Cystamine v Control
- cys_vs_cys_2b_5HT: Cystamine v (Cystamine + 5-HT)
- cys_vs_lex_2b_5HT: Cystamine v (escitalopram + 5-HT)
- cys_vs_lex: Cystamine v escitalopram
- lex_2b_5HT_vs_5HT: (escitalopram + 5-HT) v 5-HT
- lex_2b_5HT_vs_Ctrl: (escitalopram + 5-HT) v Control
- lex_2b_5HT_vs_cys_2b_5HT: (escitalopram + 5-HT) v (Cystamine + 5-HT)
- lex_2b_5HT_vs_cys: (escitalopram + 5-HT) v Cystamine
- lex_2b_5HT_vs_lex: (escitalopram + 5-HT) v escitalopram
- lex_vs_5HT: escitalopram v 5-HT
- lex_vs_Ctrl: escitalopram v Control
- lex_vs_cys_2b_5HT: escitalopram v (Cystamine + 5-HT)
- lex_vs_cys: escitalopram v Cystamine
- lex_vs_lex_2b_5HT: escitalopram v (escitalopram + 5-HT)
Full list of the 90 filenames:
5HT_vs_Ctrl_DESeq2_fulltable.xlsx
5HT_vs_Ctrl_padj0.05_FC1_DEG9.xlsx
5HT_vs_Ctrl_padj0.05_FC2_DEG9.xlsx
5HT_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
5HT_vs_cys_2b_5HT_padj0.05_FC1_DEG2897.xlsx
5HT_vs_cys_2b_5HT_padj0.05_FC2_DEG2732.xlsx
5HT_vs_cys_DESeq2_fulltable.xlsx
5HT_vs_cys_padj0.05_FC1_DEG2949.xlsx
5HT_vs_cys_padj0.05_FC2_DEG2787.xlsx
5HT_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
5HT_vs_lex_2b_5HT_padj0.05_FC1_DEG240.xlsx
5HT_vs_lex_2b_5HT_padj0.05_FC2_DEG225.xlsx
5HT_vs_lex_DESeq2_fulltable.xlsx
5HT_vs_lex_padj0.05_FC1_DEG735.xlsx
5HT_vs_lex_padj0.05_FC2_DEG682.xlsx
Ctrl_vs_5HT_DESeq2_fulltable.xlsx
Ctrl_vs_5HT_padj0.05_FC1_DEG9.xlsx
Ctrl_vs_5HT_padj0.05_FC2_DEG9.xlsx
Ctrl_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
Ctrl_vs_cys_2b_5HT_padj0.05_FC1_DEG2277.xlsx
Ctrl_vs_cys_2b_5HT_padj0.05_FC2_DEG2150.xlsx
Ctrl_vs_cys_DESeq2_fulltable.xlsx
Ctrl_vs_cys_padj0.05_FC1_DEG2293.xlsx
Ctrl_vs_cys_padj0.05_FC2_DEG2165.xlsx
Ctrl_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
Ctrl_vs_lex_2b_5HT_padj0.05_FC1_DEG132.xlsx
Ctrl_vs_lex_2b_5HT_padj0.05_FC2_DEG123.xlsx
Ctrl_vs_lex_DESeq2_fulltable.xlsx
Ctrl_vs_lex_padj0.05_FC1_DEG413.xlsx
Ctrl_vs_lex_padj0.05_FC2_DEG396.xlsx
cys_2b_5HT_vs_5HT_DESeq2_fulltable.xlsx
cys_2b_5HT_vs_5HT_padj0.05_FC1_DEG2897.xlsx
cys_2b_5HT_vs_5HT_padj0.05_FC2_DEG2732.xlsx
cys_2b_5HT_vs_Ctrl_DESeq2_fulltable.xlsx
cys_2b_5HT_vs_Ctrl_padj0.05_FC1_DEG2277.xlsx
cys_2b_5HT_vs_Ctrl_padj0.05_FC2_DEG2150.xlsx
cys_2b_5HT_vs_cys_DESeq2_fulltable.xlsx
cys_2b_5HT_vs_cys_padj0.05_FC1_DEG5.xlsx
cys_2b_5HT_vs_cys_padj0.05_FC2_DEG5.xlsx
cys_2b_5HT_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
cys_2b_5HT_vs_lex_2b_5HT_padj0.05_FC1_DEG1887.xlsx
cys_2b_5HT_vs_lex_2b_5HT_padj0.05_FC2_DEG1802.xlsx
cys_2b_5HT_vs_lex_DESeq2_fulltable.xlsx
cys_2b_5HT_vs_lex_padj0.05_FC1_DEG1942.xlsx
cys_2b_5HT_vs_lex_padj0.05_FC2_DEG1839.xlsx
cys_vs_5HT_DESeq2_fulltable.xlsx
cys_vs_5HT_padj0.05_FC1_DEG2949.xlsx
cys_vs_5HT_padj0.05_FC2_DEG2787.xlsx
cys_vs_Ctrl_DESeq2_fulltable.xlsx
cys_vs_Ctrl_padj0.05_FC1_DEG2293.xlsx
cys_vs_Ctrl_padj0.05_FC2_DEG2165.xlsx
cys_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
cys_vs_cys_2b_5HT_padj0.05_FC1_DEG5.xlsx
cys_vs_cys_2b_5HT_padj0.05_FC2_DEG5.xlsx
cys_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
cys_vs_lex_2b_5HT_padj0.05_FC1_DEG1892.xlsx
cys_vs_lex_2b_5HT_padj0.05_FC2_DEG1810.xlsx
cys_vs_lex_DESeq2_fulltable.xlsx
cys_vs_lex_padj0.05_FC1_DEG1805.xlsx
cys_vs_lex_padj0.05_FC2_DEG1715.xlsx
lex_2b_5HT_vs_5HT_DESeq2_fulltable.xlsx
lex_2b_5HT_vs_5HT_padj0.05_FC1_DEG240.xlsx
lex_2b_5HT_vs_5HT_padj0.05_FC2_DEG225.xlsx
lex_2b_5HT_vs_Ctrl_DESeq2_fulltable.xlsx
lex_2b_5HT_vs_Ctrl_padj0.05_FC1_DEG132.xlsx
lex_2b_5HT_vs_Ctrl_padj0.05_FC2_DEG123.xlsx
lex_2b_5HT_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
lex_2b_5HT_vs_cys_2b_5HT_padj0.05_FC1_DEG1887.xlsx
lex_2b_5HT_vs_cys_2b_5HT_padj0.05_FC2_DEG1802.xlsx
lex_2b_5HT_vs_cys_DESeq2_fulltable.xlsx
lex_2b_5HT_vs_cys_padj0.05_FC1_DEG1892.xlsx
lex_2b_5HT_vs_cys_padj0.05_FC2_DEG1810.xlsx
lex_2b_5HT_vs_lex_DESeq2_fulltable.xlsx
lex_2b_5HT_vs_lex_padj0.05_FC1_DEG18.xlsx
lex_2b_5HT_vs_lex_padj0.05_FC2_DEG18.xlsx
lex_vs_5HT_DESeq2_fulltable.xlsx
lex_vs_5HT_padj0.05_FC1_DEG735.xlsx
lex_vs_5HT_padj0.05_FC2_DEG682.xlsx
lex_vs_Ctrl_DESeq2_fulltable.xlsx
lex_vs_Ctrl_padj0.05_FC1_DEG413.xlsx
lex_vs_Ctrl_padj0.05_FC2_DEG396.xlsx
lex_vs_cys_2b_5HT_DESeq2_fulltable.xlsx
lex_vs_cys_2b_5HT_padj0.05_FC1_DEG1942.xlsx
lex_vs_cys_2b_5HT_padj0.05_FC2_DEG1839.xlsx
lex_vs_cys_DESeq2_fulltable.xlsx
lex_vs_cys_padj0.05_FC1_DEG1805.xlsx
lex_vs_cys_padj0.05_FC2_DEG1715.xlsx
lex_vs_lex_2b_5HT_DESeq2_fulltable.xlsx
lex_vs_lex_2b_5HT_padj0.05_FC1_DEG18.xlsx
lex_vs_lex_2b_5HT_padj0.05_FC2_DEG18.xlsx
The RNA sequencing was performed by the staff members of the Yale Center for Genomic Analysis, whose center is supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number 1S10OD030363-01A1.
Code/software
Microsoft Excel or other software that can read Excel files.
Access information
N/A.
Human subjects data
Term placentas were collected anonymously from patients undergoing elective repeat Cesarian sections who delivered healthy babies. All the women who provided term placental samples signed an informed consent (Yale IRB protocol 1208010742). All data has been de-identified.
Specimens
Term placentas were collected anonymously from patients undergoing elective repeat Cesarian sections who delivered healthy babies. All the women who provided term placental samples signed an informed consent (Yale IRB protocol 1208010742).
Trophoblast Purification
Cytotrophoblast were prepared from fresh human term placentas by trypsin digestion and Percoll gradient fractionation, with the addition of an anti-CD9 and CD45 magnetic bead purification step, as previously described (1,2). During the initial steps of the digestions and up to the magnetic purification step, 10% fetal bovine serum (FBS, Gemini Bio-Products, Broderick, CA, 100-106) diluted in DMEM/F12 (Gibco, ThermoFisher Scientific, Waltham, MA, 11330-032) with 4 mM L-glutamine, 1% penicillin/streptomycin was utilized. After the magnetic purification step, no FBS was added to the culture media, unless specifically noted. Cytotrophoblasts were then diluted to 1x106 cells per ml in DMEM/F12 with 4 mM L-glutamine, 1% penicillin/streptomycin and either: 1) pelleted immediately by centrifugation for a zero-time point; 2) cultured in two- or four-chamber Nunc™ Lab-Tek™ II Chamber Slide™ System slides (ThermoFisher Scientific) or six-wells plates (CELLSTAR® #657160 6-well cell culture plates) for 24-96 hours in humidified 5% CO2-95% air at 37˚C; or 3) and used for additional studies as described below.
RNA sequencing
RNA Seq Quality Control: Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by Nanodrop (Nanodrop, ND-1000, ThermoFisher Scientific). RNA integrity was determined by running an Agilent Bioanalyzer 2100 gel, which measures the ratio of the ribosomal peaks.
RNA Seq Library Prep: Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351, Roche Diagnostics, Indianapolis, IN), rRNA was depleted starting from a normalized input of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed toDNA. Samples were then fragmented using heat and magnesium. 1st strand synthesis was performed using random priming. 2nd strand synthesis incorporated dUTPs into the 2nd strand cDNA. Adapters were then ligated, and the library was amplified. Strands marked with dUTPs were not amplified allowing for strand-specific sequencing. Indexed libraries that meet appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Library Quant Kit, Roche Diagnostics, 07960298001) and insert size distribution determined with an Agilent Bioanalyzer (Agilent TapeStation 4200). Samples with a yield of ≥0.5 ng/µl were used for sequencing.
Flow Cell Preparation and Sequencing: Sample concentrations were normalized to 2.0 nM and loaded onto an Illumina NovaSeq (San Diego, CA) flow cell at a concentration that yields 35 million passing filter clusters per sample. Samples were sequenced using 100bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols. The 10bpunique dual index was read during additional sequencing reads that automatically follow the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the Yale Center for Genomic Analysis (New Haven, CT) high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.
Data Analysis and Storage: Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Base calls were transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis—sample de-multiplexing and alignment to the human genome—was performed using Illumina's CASAVA 1.8.2 software suite. The data were returned to the user if the sample error rate was less than 2% and the distribution of reads per sample in a lane was within reasonable tolerance. Data was retained on the cluster for at least 6 months, after which it was transferred to a tape backup system.
Following RNA sequencing, low quality reads were trimmed, and adaptor contamination were removed using Trim Galore (v0.5.0; Babraham Bioinformatics, Cambridge, UK). Trimmed reads were mapped to the human reference genome (mm10) using HISAT2 (v2.1.0) (3). Gene expression levels were quantified using StringTie (v1.3.3b) (4) with gene models (v27) from the GENCODE project (5). Differentially expressed genes were identified using DESeq2 (v 1.22.1) (6). Transcripts per million (TPM) were calculated as previously described (7), while adjusted p values were calculated with DESeq2 using the Benjamini and Hochberg method (8).
References
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2. Tang Z, Tadesse S, Norwitz E, Mor G, Abrahams VM, Guller S. Isolation of hofbauer cells from human term placentas with high yield and purity. Am J Reprod Immunol. 2011;66(4):336-348.
3. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907-915.
4. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290-295.
5. Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, Garcia Giron C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martinez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47(D1):D766-D773.
6. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
7. Zhao Y, Li MC, Konate MM, Chen L, Das B, Karlovich C, Williams PM, Evrard YA, Doroshow JH, McShane LM. TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository. J Transl Med. 2021;19(1):269.
8. Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med. 1990;9(7):811-818.