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26 changes: 13 additions & 13 deletions README.md
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In this manuscript, several transcriptome data sets generated by different technologies were included. To minimize platform and processing differences, raw fastq files of public datasets using the Illumina sequencing platform were downloaded and re-processed.


- Cinkornpumin, J.K., Kwon, S.Y., Guo, Y., Hossain, I., Sirois, J., Russett, C.S., Tseng, H.-W., Okae, H., Arima, T., Duchaine, T.F., et al. (2020). **[Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and methylome](https://jlduan.github.io/Replica/j.stemcr.2020.06.003/)**. Stem Cell Reports 15, 198–213.
- Dong, C., Beltcheva, M., Gontarz, P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K.-M., Yoon, E.-J., Xing, X., et al. (2020). **[Derivation of trophoblast stem cells from naïve human pluripotent stem cells](https://jlduan.github.io/Replica/eLife.52504)**. Elife 9.
- Linneberg-Agerholm, M., Wong, Y.F., Romero Herrera, J.A., Monteiro, R.S., Anderson, K.G.V., and Brickman, J.M. (2019). **[Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm](https://jlduan.github.io/Replica/dev.180620/)**. Development 146.
- Lv, B., An, Q., Zeng, Q., Zhang, X., Lu, P., Wang, Y., Zhu, X., Ji, Y., Fan, G., and Xue, Z. (2019). **[Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses](https://jlduan.github.io/Replica/journal.pbio.3000187)**. PLoS Biol. 17, e3000187.
- Nakamura, T., Okamoto, I., Sasaki, K., Yabuta, Y., Iwatani, C., Tsuchiya, H., Seita, Y., Nakamura, S., Yamamoto, T., and Saitou, M. (2016). **[A developmental coordinate of pluripotency among mice, monkeys and humans](https://jlduan.github.io/Replica/nature19096)**. Nature 537, 57–62.
- Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S.P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., and Lanner, F. (2016). **[Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos](https://jlduan.github.io/Replica/j.cell.2016.03.023)**. Cell 165, 1012–1026.
- Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014). **[Resetting transcription factor control circuitry toward ground-state pluripotency in human](https://jlduan.github.io/Replica/j.cell.2014.08.029)**. Cell 158, 1254–1269.
- Xiang, L., Yin, Y., Zheng, Y., Ma, Y., Li, Y., Zhao, Z., Guo, J., Ai, Z., Niu, Y., Duan, K., et al. (2020). **[A developmental landscape of 3D-cultured human pre-gastrulation embryos](https://jlduan.github.io/Replica/s41586-019-1875-y)**. Nature 577, 537–542.
- Zhou, F., Wang, R., Yuan, P., Ren, Y., Mao, Y., Li, R., Lian, Y., Li, J., Wen, L., Yan, L., et al. (2019). **[Reconstituting the transcriptome and DNA methylome landscapes of human implantation](https://jlduan.github.io/Replica/s41586-019-1500-0)**. Nature 572, 660–664.
- Cinkornpumin, J.K., Kwon, S.Y., Guo, Y., Hossain, I., Sirois, J., Russett, C.S., Tseng, H.-W., Okae, H., Arima, T., Duchaine, T.F., et al. (2020). **[Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and methylome](https://jlduan.github.io/replica/j.stemcr.2020.06.003/)**. Stem Cell Reports 15, 198–213.
- Dong, C., Beltcheva, M., Gontarz, P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K.-M., Yoon, E.-J., Xing, X., et al. (2020). **[Derivation of trophoblast stem cells from naïve human pluripotent stem cells](https://jlduan.github.io/replica/eLife.52504)**. Elife 9.
- Linneberg-Agerholm, M., Wong, Y.F., Romero Herrera, J.A., Monteiro, R.S., Anderson, K.G.V., and Brickman, J.M. (2019). **[Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm](https://jlduan.github.io/replica/dev.180620/)**. Development 146.
- Lv, B., An, Q., Zeng, Q., Zhang, X., Lu, P., Wang, Y., Zhu, X., Ji, Y., Fan, G., and Xue, Z. (2019). **[Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses](https://jlduan.github.io/replica/journal.pbio.3000187)**. PLoS Biol. 17, e3000187.
- Nakamura, T., Okamoto, I., Sasaki, K., Yabuta, Y., Iwatani, C., Tsuchiya, H., Seita, Y., Nakamura, S., Yamamoto, T., and Saitou, M. (2016). **[A developmental coordinate of pluripotency among mice, monkeys and humans](https://jlduan.github.io/replica/nature19096)**. Nature 537, 57–62.
- Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S.P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., and Lanner, F. (2016). **[Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos](https://jlduan.github.io/replica/j.cell.2016.03.023)**. Cell 165, 1012–1026.
- Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014). **[Resetting transcription factor control circuitry toward ground-state pluripotency in human](https://jlduan.github.io/replica/j.cell.2014.08.029)**. Cell 158, 1254–1269.
- Xiang, L., Yin, Y., Zheng, Y., Ma, Y., Li, Y., Zhao, Z., Guo, J., Ai, Z., Niu, Y., Duan, K., et al. (2020). **[A developmental landscape of 3D-cultured human pre-gastrulation embryos](https://jlduan.github.io/replica/s41586-019-1875-y)**. Nature 577, 537–542.
- Zhou, F., Wang, R., Yuan, P., Ren, Y., Mao, Y., Li, R., Lian, Y., Li, J., Wen, L., Yan, L., et al. (2019). **[Reconstituting the transcriptome and DNA methylome landscapes of human implantation](https://jlduan.github.io/replica/s41586-019-1500-0)**. Nature 572, 660–664.


***

Related publications:

- Yanagida, A., Spindlow, D., Nichols, J., Dattani, A., Smith, A., and Guo, G. (2021). [Naive stem cell blastocyst model captures human embryo lineage segregation](https://jlduan.github.io/Replica/j.stem.2021.04.031). Cell Stem Cell 28, 1016–1022.e4.
- Fan, Y., Min, Z., Alsolami, S., Ma, Z., Zhang, E., Chen, W., Zhong, K., Pei, W., Kang, X., Zhang, P., et al. (2021). [Generation of human blastocyst-like structures from pluripotent stem cells](https://jlduan.github.io/Replica/s41421-021-00316-8). Cell Discov 7, 81.
- Sozen, B., Jorgensen, V., Weatherbee, B.A.T., Chen, S., Zhu, M., and Zernicka-Goetz, M. (2021). [Reconstructing aspects of human embryogenesis with pluripotent stem cells](https://jlduan.github.io/Replica/s41467-021-25853-4). Nat. Commun. 12, 5550.
- Kagawa, H., Javali, A., Khoei, H.H., Sommer, T.M., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Castel, G., Bruneau, A., Maenhoudt, N., et al. (2021). [Human blastoids model blastocyst development and implantation](https://jlduan.github.io/Replica/s41586-021-04267-8). Nature 1–9.
- Yanagida, A., Spindlow, D., Nichols, J., Dattani, A., Smith, A., and Guo, G. (2021). [Naive stem cell blastocyst model captures human embryo lineage segregation](https://jlduan.github.io/replica/j.stem.2021.04.031). Cell Stem Cell 28, 1016–1022.e4.
- Fan, Y., Min, Z., Alsolami, S., Ma, Z., Zhang, E., Chen, W., Zhong, K., Pei, W., Kang, X., Zhang, P., et al. (2021). [Generation of human blastocyst-like structures from pluripotent stem cells](https://jlduan.github.io/replica/s41421-021-00316-8). Cell Discov 7, 81.
- Sozen, B., Jorgensen, V., Weatherbee, B.A.T., Chen, S., Zhu, M., and Zernicka-Goetz, M. (2021). [Reconstructing aspects of human embryogenesis with pluripotent stem cells](https://jlduan.github.io/replica/s41467-021-25853-4). Nat. Commun. 12, 5550.
- Kagawa, H., Javali, A., Khoei, H.H., Sommer, T.M., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Castel, G., Bruneau, A., Maenhoudt, N., et al. (2021). [Human blastoids model blastocyst development and implantation](https://jlduan.github.io/replica/s41586-021-04267-8). Nature 1–9.


<br>
36 changes: 18 additions & 18 deletions notebooks/compare_blastoids.html
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<p><br></p>
<p>In this manuscript, several transcriptome data sets generated by different technologies were included. To minimize platform and processing differences, raw fastq files of public datasets using the Illumina sequencing platform were downloaded and re-processed.</p>
<ul>
<li>Cinkornpumin, J.K., Kwon, S.Y., Guo, Y., Hossain, I., Sirois, J., Russett, C.S., Tseng, H.-W., Okae, H., Arima, T., Duchaine, T.F., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/Replica/j.stemcr.2020.06.003/">Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and methylome</a></strong>. Stem Cell Reports 15, 198–213.</li>
<li>Dong, C., Beltcheva, M., Gontarz, P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K.-M., Yoon, E.-J., Xing, X., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/Replica/eLife.52504">Derivation of trophoblast stem cells from naïve human pluripotent stem cells</a></strong>. Elife 9.</li>
<li>Linneberg-Agerholm, M., Wong, Y.F., Romero Herrera, J.A., Monteiro, R.S., Anderson, K.G.V., and Brickman, J.M. (2019). <strong><a href="https://jlduan.github.io/Replica/dev.180620/">Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm</a></strong>. Development 146.</li>
<li>Lv, B., An, Q., Zeng, Q., Zhang, X., Lu, P., Wang, Y., Zhu, X., Ji, Y., Fan, G., and Xue, Z. (2019). <strong><a href="https://jlduan.github.io/Replica/journal.pbio.3000187">Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses</a></strong>. PLoS Biol. 17, e3000187.</li>
<li>Nakamura, T., Okamoto, I., Sasaki, K., Yabuta, Y., Iwatani, C., Tsuchiya, H., Seita, Y., Nakamura, S., Yamamoto, T., and Saitou, M. (2016). <strong><a href="https://jlduan.github.io/Replica/nature19096">A developmental coordinate of pluripotency among mice, monkeys and humans</a></strong>. Nature 537, 57–62.</li>
<li>Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S.P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., and Lanner, F. (2016). <strong><a href="https://jlduan.github.io/Replica/j.cell.2016.03.023">Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos</a></strong>. Cell 165, 1012–1026.</li>
<li>Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al.&nbsp;(2014). <strong><a href="https://jlduan.github.io/Replica/j.cell.2014.08.029">Resetting transcription factor control circuitry toward ground-state pluripotency in human</a></strong>. Cell 158, 1254–1269.</li>
<li>Xiang, L., Yin, Y., Zheng, Y., Ma, Y., Li, Y., Zhao, Z., Guo, J., Ai, Z., Niu, Y., Duan, K., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/Replica/s41586-019-1875-y/">A developmental landscape of 3D-cultured human pre-gastrulation embryos</a></strong>. Nature 577, 537–542.</li>
<li>Zhou, F., Wang, R., Yuan, P., Ren, Y., Mao, Y., Li, R., Lian, Y., Li, J., Wen, L., Yan, L., et al.&nbsp;(2019). <strong><a href="https://jlduan.github.io/Replica/s41586-019-1500-0">Reconstituting the transcriptome and DNA methylome landscapes of human implantation</a></strong>. Nature 572, 660–664.</li>
<li>Cinkornpumin, J.K., Kwon, S.Y., Guo, Y., Hossain, I., Sirois, J., Russett, C.S., Tseng, H.-W., Okae, H., Arima, T., Duchaine, T.F., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/replica/j.stemcr.2020.06.003/">Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and methylome</a></strong>. Stem Cell Reports 15, 198–213.</li>
<li>Dong, C., Beltcheva, M., Gontarz, P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K.-M., Yoon, E.-J., Xing, X., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/replica/eLife.52504">Derivation of trophoblast stem cells from naïve human pluripotent stem cells</a></strong>. Elife 9.</li>
<li>Linneberg-Agerholm, M., Wong, Y.F., Romero Herrera, J.A., Monteiro, R.S., Anderson, K.G.V., and Brickman, J.M. (2019). <strong><a href="https://jlduan.github.io/replica/dev.180620/">Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm</a></strong>. Development 146.</li>
<li>Lv, B., An, Q., Zeng, Q., Zhang, X., Lu, P., Wang, Y., Zhu, X., Ji, Y., Fan, G., and Xue, Z. (2019). <strong><a href="https://jlduan.github.io/replica/journal.pbio.3000187">Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses</a></strong>. PLoS Biol. 17, e3000187.</li>
<li>Nakamura, T., Okamoto, I., Sasaki, K., Yabuta, Y., Iwatani, C., Tsuchiya, H., Seita, Y., Nakamura, S., Yamamoto, T., and Saitou, M. (2016). <strong><a href="https://jlduan.github.io/replica/nature19096">A developmental coordinate of pluripotency among mice, monkeys and humans</a></strong>. Nature 537, 57–62.</li>
<li>Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S.P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., and Lanner, F. (2016). <strong><a href="https://jlduan.github.io/replica/j.cell.2016.03.023">Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos</a></strong>. Cell 165, 1012–1026.</li>
<li>Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al.&nbsp;(2014). <strong><a href="https://jlduan.github.io/replica/j.cell.2014.08.029">Resetting transcription factor control circuitry toward ground-state pluripotency in human</a></strong>. Cell 158, 1254–1269.</li>
<li>Xiang, L., Yin, Y., Zheng, Y., Ma, Y., Li, Y., Zhao, Z., Guo, J., Ai, Z., Niu, Y., Duan, K., et al.&nbsp;(2020). <strong><a href="https://jlduan.github.io/replica/s41586-019-1875-y/">A developmental landscape of 3D-cultured human pre-gastrulation embryos</a></strong>. Nature 577, 537–542.</li>
<li>Zhou, F., Wang, R., Yuan, P., Ren, Y., Mao, Y., Li, R., Lian, Y., Li, J., Wen, L., Yan, L., et al.&nbsp;(2019). <strong><a href="https://jlduan.github.io/replica/s41586-019-1500-0">Reconstituting the transcriptome and DNA methylome landscapes of human implantation</a></strong>. Nature 572, 660–664.</li>
</ul>
<p><br></p>
<hr>
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<ul>
<li>BioProject Accession: PRJEB11202</li>
<li>ArrayExpress: E-MTAB-3929</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/j.cell.2016.03.023">https://jlduan.github.io/Replica/j.cell.2016.03.023</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/j.cell.2016.03.023">https://jlduan.github.io/replica/j.cell.2016.03.023</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA562548</li>
<li>GEO Accession: GSE136447</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/s41586-019-1875-y">https://jlduan.github.io/Replica/s41586-019-1875-y</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/s41586-019-1875-y">https://jlduan.github.io/replica/s41586-019-1875-y</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA431392</li>
<li>GEO Accession: GSE109555</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/s41586-019-1500-0">https://jlduan.github.io/Replica/s41586-019-1500-0</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/s41586-019-1500-0">https://jlduan.github.io/replica/s41586-019-1500-0</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJEB7132</li>
<li>ArrayExpress Accession: E-MTAB-2857</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/j.cell.2014.08.029">https://jlduan.github.io/Replica/j.cell.2014.08.029</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/j.cell.2014.08.029">https://jlduan.github.io/replica/j.cell.2014.08.029</a>
</li>
</ul>
<div class="cell">
Expand All @@ -2990,7 +2990,7 @@
<ul>
<li>BioProject Accession: PRJNA576801</li>
<li>GEO Accession: GSE138688</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/eLife.52504">https://jlduan.github.io/Replica/eLife.52504</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/eLife.52504">https://jlduan.github.io/replica/eLife.52504</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA638350</li>
<li>GEO Accession: GSE152101</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/j.stemcr.2020.06.003">https://jlduan.github.io/Replica/j.stemcr.2020.06.003</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/j.stemcr.2020.06.003">https://jlduan.github.io/replica/j.stemcr.2020.06.003</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA516921</li>
<li>GEO Accession: GSE125616</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/journal.pbio.3000187/">https://jlduan.github.io/Replica/journal.pbio.3000187</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/journal.pbio.3000187/">https://jlduan.github.io/replica/journal.pbio.3000187</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA574150</li>
<li>GEO Accession: GSE138012</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/dev.180620">https://jlduan.github.io/Replica/dev.180620</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/dev.180620">https://jlduan.github.io/replica/dev.180620</a>
</li>
</ul>
<div class="cell">
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<ul>
<li>BioProject Accession: PRJNA301445</li>
<li>GEO Accession: GSE74767</li>
<li>Notebook: <a href="https://jlduan.github.io/Replica/nature19096">https://jlduan.github.io/Replica/nature19096</a>
<li>Notebook: <a href="https://jlduan.github.io/replica/nature19096">https://jlduan.github.io/replica/nature19096</a>
</li>
</ul>
<section id="data-loading-1" class="level2"><h2 class="anchored" data-anchor-id="data-loading-1">Data loading</h2>
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