Sequencing Data (RNA) | Arrays (Methylation) | Supplemental Data
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Sequencing Data (RNA-seq)
Sequencing Data (RNA-seq)
Species: Homo sapien
Samples: 167 total placenta samples: 124 first trimester placentas (59 females, 65 males) and 43 third trimester placentas (18 females, 25 males). All pregnancies resulted in live, healthy babies.
RNA isolation: AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN), which uses two spin columns to elute genomic DNA and total RNA (including small RNAs) separately.
Citation:
Citation:
Gonzalez TL et al 2024. "High-throughput mRNA-seq atlas of human placenta shows vast transcriptome remodeling from first to third trimester." Biology of Reproduction, 2024 Jan 25;ioae007. Online ahead of print. [PMID: 38271627]
NCBI GEO GSE131696 (part of NCBI GEO superseries GSE131875)
Species: Homo sapien
Source: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester.
Samples: 3 female and 3 male samples (the placenta is genetically fetal since it develops from the trophectoderm). All pregnancies resulted in live, healthy babies.
RNA isolation: single cell droplet based method after cell sorting
Citation:
Citation:
Sun & Gonzalez et al 2020, "Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface", J Clin Endocrinol Metab. 2020 Dec 1;105(12):e4831-e4847. doi: 10.1210/clinem/dgaa503. [PMID: 32772088, PMCID: PMC7571453]
Preprint (with more details about methods and the maternal/fetal bulk RNA-seq) available at: "The maternal-fetal interface of successful pregnancies and impact of fetal sex using single cell sequencing", BioRxiv. Everything is correct and it is the same data. The final version was re-written to focus on sex differences.
Accepted, pre-proof version available at PubMed Central under PMCID: PMC7571453. The citations to our supplemental information at FigShare were scrambled in the pre-proof and fixed after this version.
Supplemental information: https://doi.org/10.6084/m9.figshare.c.4741742.v2 (version 2 due to addition of a file during the peer review process).
Final published version on JCEM or ResearchGate.
Demographics are Table S1, hosted on FigShare.com at https://doi.org/10.6084/m9.figshare.10314425.v1
NCBI GEI GSE131874 (part of NCBI GEO superseries GSE131875)
Species: Homo sapien
Source: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester. Tissue was separated into matched samples of placenta (fetal origin) and decidua (maternal origin, hormone-transformed uterine lining during pregnancy).
Samples: 4 placenta and 4 decidua from 4 pregnancies (2 with female fetus, 2 with male fetus). All pregnancies resulted in live, healthy babies.
RNA isolation: AllPrep DNA/RNA kit (QIAGEN), which uses two spin columns to elute genomic DNA and total RNA separately.
Citation:
Citation:
Sun T & Gonzalez TL, et al 2020, "Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface", J Clin Endocrinol Metab. 2020 Dec 1;105(12):e4831-e4847. doi: 10.1210/clinem/dgaa503. [PMID: 32772088]
(See above for details)
NCBI GEO GSE109082
Species: Homo sapien
Source: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester. Tissue was separated to recover placenta (fetal origin).
Samples: n=39 placenta samples (17 females, 22 males). All pregnancies resulted in live, healthy babies.
RNA isolation: AllPrep DNA/RNA kit (QIAGEN), which uses two spin columns to elute genomic DNA and total RNA separately.
Beware: 38 of these 39 samples were re-sequenced and submitted in GSE215421 (see below), so don't combine data or you will be double-counting some placentas.
Citations:
Citations:
Gonzalez, T.L., Sun, T., Koeppel, A.F. et al. "Sex differences in the late first trimester human placenta transcriptome." Biology of Sex Differences, 2018, 9, 4. https://doi.org/10.1186/s13293-018-0165-y [PMID: 29335024] -- original highly cited paper
Gonzalez TL, Willson BE, Wang ET, Taylor KD, Novoa A, Swarna A, Ortiz JC, Zeno GJ, Jefferies CA, Lawrenson K, Rotter JI, Chen YDI, Williams J III, Cui J, Goodarzi MO, Pisarska MD. “Sexually dimorphic DNA methylation and gene expression patterns in human first trimester placenta” Biology of Sex Differences, 2024 Aug 16;15(1):63. [PMID: 39152463; PMCID: PMC11328442] -- follow up paper
NCBI GEO GSE215421
Species: Homo sapien
Source: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester. Tissue was separated to recover placenta (fetal origin) and remove decidua (maternal origin).
Samples: n=141 placenta samples, including from pregnancies conceived with infertility (n=33 NIFT, n=34 IVF) and natural conceptions (n=74). All pregnancies resulted in live, healthy babies.
Beware: this analysis includes the natural conception samples from GSE109082 (raw counts re-created with Kallisto from raw data) and GSE131874 (same RNA but re-sequenced).
RNA isolation: AllPrep DNA/RNA kit (QIAGEN), which uses two spin columns to elute genomic DNA and total RNA separately.
Citations:
Citations:
Lee B, Koeppel AF, Wang ET, Gonzalez TL, Sun T, Kroener L, Lin Y, Joshi NV, Ghadiali T, Turner SD, Rich SS, Farber CR, Rotter JI, Ida Chen YD, Goodarzi MO, Guller S, Harwood B, Serna TB, Williams J 3rd, Pisarska MD. “Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies.” Fertility and Sterility, 2019 Jan 2. S0015-0282(18)32200-3. [PMID: 30611556; PMCID: PMC7156023] -- infertility analysis
Gonzalez TL, Willson BE, Wang ET, Taylor KD, Novoa A, Swarna A, Ortiz JC, Zeno GJ, Jefferies CA, Lawrenson K, Rotter JI, Chen YDI, Williams J III, Cui J, Goodarzi MO, Pisarska MD. “Sexually dimorphic DNA methylation and gene expression patterns in human first trimester placenta” Biology of Sex Differences, 2024 Aug 16;15(1):63. [PMID: 39152463; PMCID: PMC11328442] -- sex differences analysis
NCBI GEO GSE184860
Species: Homo sapien
Tissue type: Placenta
Source for first trimester: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester. Tissue was separated to recover placenta (fetal origin) and remove decidua (maternal origin).
Source for third trimester: Placenta discarded after delivery of a live baby. A tissue punch was collected from the fetal side near the umbillical cord insertion side beneath the amnion.
Samples: n=124 first trimester placenta (58 females, 55 males) and n=47 third trimester placenta (19 females, 28 males). All pregnancies resulted in live, healthy babies.
RNA isolation: AllPrep DNA/RNA/miRNA kit, which uses two spin columns to elute genomic DNA and total RNA separately. Small RNAs >18 bases are recovered.
Sequencing: small RNA-seq which identified two classes of small RNAs (microRNAs and piwi-RNAs).
Citations:
Citations:
Gonzalez TL, Eisman LE, Joshi NV, et al. "High-throughput miRNA sequencing of the human placenta: expression throughout gestation." Epigenomics, 2021 Jul; 13(13):995-1012. Epub 2021 May 25. https://doi.org/10.2217/epi-2021-0055 [PMID: 34030457]
Flowers AE, Gonzalez TL, Joshi NV, et al. "Sex differences in microRNA expression in first and third trimester human placenta." Biol Reprod. 2022 Mar 19; 106(3):551-567. doi: 10.1093/biolre/ioab221 [PMID: 35040930]
Array Data (DNA methylation)
Array Data (DNA methylation)
NCBI GEO GSE289196
Species: Homo sapien
Tissue type: Placenta
Source for first trimester: Tissue discarded after chorionic villus sampling, a prenatal diagnostic test that takes place in late first trimester. Tissue was separated to recover placenta (fetal origin) and remove decidua (maternal origin).
Samples: n=138 first trimester placenta (44 IVF, 38 non-IVF fertility treatments, 56 spontaneous/unassisted/control). All pregnancies resulted in live, healthy babies.
DNA isolation: AllPrep DNA/RNA/miRNA kit, which uses two spin columns to elute genomic DNA and total RNA separately.
Array: Infinium MethylationEPIC array for human DNA methylation sites (Illumina)
Array measures DNA methylation on CpG and CpH sites.
Citations:
Citations:
Gonzalez TL, Schaub AM, Lee B, Cui J, Taylor KD, Dorfman AE, Goodarzi MO, Wang ET, Chen YDI, Rotter JI, Hussaini R, Harakuni PM, Khan MH, Rich SS, Farber CR, Williams J III, Pisarska MD. "Infertility and treatments utilized have minimal effects on first trimester placenta DNA methylation and gene expression." Fertility and Sterility, 2023 Feb;119(2):301-312. [PMID: 36379261]
Gonzalez TL, Willson BE, Wang ET, Taylor KD, Novoa A, Swarna A, Ortiz JC, Zeno GJ, Jefferies CA, Lawrenson K, Rotter JI, Chen YDI, Williams J III, Cui J, Goodarzi MO, Pisarska MD. “Sexually dimorphic DNA methylation and gene expression patterns in human first trimester placenta” Biology of Sex Differences, 2024 Aug 16;15(1):63. [PMID: 39152463; PMCID: PMC11328442]
Articles and Supplemental Information
Articles and Supplemental Information
My bibliography at PubMed contains a list of all my published articles, plus PubMed links.
I upload all my articles to ResearchGate. If the journal requires it, I wait a few months after publication before making them public, but please request any article you need and I can send it to you privately.
The supplemental information is available under the research articles. Scroll past the article pdf preview.
Example: "High-throughput miRNA sequencing of the human placenta: expression throughout gestation"
Scroll past the article pdf until you see the heading "Supplementary resources". These are the downloadable supplemental files that correspond to the article above.
If something is newly published and files are not yet uploaded, go ahead and ask for publications via ResearchGate or Twitter. I am happy to share!
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