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0_readme_v2.Rmd
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---
title: "README"
date: "`r Sys.Date()`"
author:
- name: Arun Seetharam
- name: Ha Vu
affiliation: Tuteja Lab
affiliation_url: https://www.tutejalab.org
output:
rmdformats::readthedown:
self_contained: true
thumbnails: false
lightbox: true
gallery: true
highlight: tango
---
```{r setup, include=FALSE}
options(max.print = "75")
knitr::opts_chunk$set(
echo = TRUE,
collapse = TRUE,
comment = "#>",
fig.path = "assets/",
fig.width = 8,
prompt = FALSE,
tidy = FALSE,
message = FALSE,
warning = TRUE
)
knitr::opts_knit$set(width = 75)
```
## BAPvsTrophoblast_Amnion
[Tuteja Lab](https://www.tutejalab.org), Iowa State University, Ames IA-50011
## Publication
If you use the scripts from this repository in your research, please cite this publication:
_coming soon_
## Contacts
1. Project related questions: Geetu Tuteja
2. Scripts and workflow related questions: please open an [issue](https://github.com/Tuteja-Lab/BAPvsTrophoblast_Amnion/issues/new) here on GitHub.
## Documentation
1. [Section 1: Pre-processing](1_input-data-prep_v2.html)
2. [Section 2: DESeq2 analysis](2_de-analyses_v2.html)
3. [Section 3: PCA plots](3_pca-plots_v2.html)
4. [Section 4: Amnion Markers](4_heatmaps_v2.html)
5. [Section 5: snRNAseq/scRNAseq analysis](5_snRNAseq_v2.html)
5. [Section 6: Custom PCE dataset generation](6_custom-PCE_v2.html)
## Data availability
The data used in this study are publicly available:
| BioProject | Assay Type | source_name | replicates | treatment | Publication | Abbreviation |
|--------------|------------|------------------------------------------------------------|------------|-------------------------------------------------|-----------------|-----------------------|
| PRJNA605646 | RNA-Seq | Naïve H9 ESC | 2 | Naive human PSC condition | Io _et al_. | nH9_Io |
| PRJNA605646 | RNA-Seq | Naïve H9 ESC-derived nTE_D1 | 2 | ABPJ treatment for 1 day | Io _et al_. | H9_nTE_D1_Io |
| PRJNA605646 | RNA-Seq | Naïve H9 ESC-derived nTE_D2 | 2 | ABPJ treatment for 2 days | Io _et al_. | H9_nTE_D2_Io |
| PRJNA605646 | RNA-Seq | term Amnion (Cont2,3,4,4b,6,7,8,9,11,12,14,15 RNA-seq) | 2 | ABPJ treatment for 3 days | Io _et al_. | H9_nTE_D3_Io |
| PRJNA605646 | RNA-Seq | Naïve H9 ESC-derived nCT_P3 | 2 | ACE treatment | Io _et al_. | H9_nCT_P3_Io |
| PRJNA605646 | RNA-Seq | Naïve H9 ESC-derived nCT_P10 | 2 | ACE treatment | Io _et al_. | H9_nCT_P10_Io |
| PRJNA605646 | RNA-Seq | Naïve H9 ESC-derived nCT_P15 | 2 | ACE treatment | Io _et al_. | H9_nCT_P15_Io |
| PRJNA605646 | RNA-Seq | Naïve PSC (Guo _et al_. Development 2017)-derived nCT_P15 | 2 | ACE treatment | Io _et al_. | cR_nCT_P15_Io |
| PRJNA605646 | RNA-Seq | 409B2 hiPSC-derived nCT_P15 | 2 | ACE treatment | Io _et al_. | iPS_nCT_P15_Io |
| PRJNA605646 | RNA-Seq | 1st Trimester_TSC (Okae _et al_) (CT30) | 2 | Okae _et al_. Cell Stem Cell 2018 | Io _et al_. | CT_TSC_Okae |
| PRJNA605646 | RNA-Seq | nST from Naïve H9 ESC-derived nCT | 2 | modified from Okae et al. Cell Stem Cell 2018 | Io _et al_. | H9_nSCT_Io |
| PRJNA605646 | RNA-Seq | nEVT from Naïve H9 ESC-derived nCT | 2 | modified from Okae et al. Cell Stem Cell 2018 | Io _et al_. | H9_nEVT_Io |
| PRJNA605646 | RNA-Seq | Primed H9 ESC | 2 | primed human PSC condition | Io _et al_. | pH9_Io |
| PRJNA605646 | RNA-Seq | pBAP_D1 from Primed H9 ESC | 2 | MEF-CM with BAP treatment | Io _et al_. | H9_pBAP_D1_Io |
| PRJNA605646 | RNA-Seq | pBAP_D2 from Primed H9 ESC | 2 | MEF-CM with BAP treatment | Io _et al_. | H9_pBAP_D2_Io |
| PRJNA605646 | RNA-Seq | pBAP_D3 from Primed H9 ESC | 2 | MEF-CM with BAP treatment | Io _et al_. | H9_pBAP_D3_Io |
| PRJNA605646 | RNA-Seq | Cytotrophoblast at 7 gestational weeks | 2 | 7 gestational weeks | Io _et al_. | CT_7wk |
| PRJNA605646 | RNA-Seq | Cytotrophoblast at 9 gestational weeks | 1 | 9 gestational weeks | Io _et al_. | CT_9wk |
| PRJNA605646 | RNA-Seq | Cytotrophoblast at 11 gestational weeks | 1 | 11 gestational weeks | Io _et al_. | CT_11wk |
| PRJNA294733 | RNA-Seq | H1 ESC-derived TB_BAP D8 (large cells, >70 μm) | 3 | BAP treatment | Yabe _et al_. | H1_BAP_D8_>70_Yabe |
| PRJNA294733 | RNA-Seq | H1 ESC-derived TB_BAP D8 (between 40-70 μm) | 3 | BAP treatment | Yabe _et al_. | H1_BAP_D8_40-70_Yabe |
| PRJNA294733 | RNA-Seq | H1 ESC-derived TB_BAP D8 (small cells, <40 μm) | 3 | BAP treatment | Yabe _et al_. | H1_BAP_D8_<40_Yabe |
| PRJNA294733 | RNA-Seq | undifferentiated H1 ESC | 3 | MEF-CM with FGF2 treatment | Yabe _et al_. | H1_Yabe |
| E-MTAB-10429 | RNA-Seq | Blastocyst_TSC (Okae _et al_) (BTS5, BTS11) | 2 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | BTS_TSC_Okae |
| E-MTAB-10429 | RNA-Seq | 1st Trimester_TSC (Okae _et al_) (CT27, CT29, CT30) | 3 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | CT_TSC_Okae |
| E-MTAB-10429 | RNA-Seq | Blastocyst_EVT (Okae _et al_) (BTS5, BTS11) | 2 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | BTS_EVT_Okae |
| E-MTAB-10429 | RNA-Seq | 1st Trimester_EVT (Okae _et al_) (CT27, CT29, CT30) | 3 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | CT_EVT_Okae |
| E-MTAB-10429 | RNA-Seq | Blastocyst_SCT (Okae _et al_) (BTS5, BTS11) | 2 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | BTS_SCT_Okae |
| E-MTAB-10429 | RNA-Seq | 1st Trimester_TSC (Okae _et al_) (CT27, CT29, CT30) | 3 | Okae _et al_. Cell Stem Cell 2018 | Sheridan _et al_. | CT_SCT_Okae |
| E-MTAB-10429 | RNA-Seq | Organoid_villous (Turco _et al_) (R053, X011, X021,X035) | 4 | Turco _et al_. Nature 2018 | Sheridan _et al_. | org_villous |
| E-MTAB-10429 | RNA-Seq | Organoid_EVT (Turco _et al_) (R053, X011, X021, x035) | 4 | Turco _et al_. Nature 2018 | Sheridan _et al_. | org_EVT |
| PRJNA352339 | RNA-Seq | undifferentiated H9 ESC, feeder free | 3 | mTeSR | Shao _et al_. | H9_ESC_Shao |
| PRJNA352339 | RNA-Seq | H9 ESC-derived amnion-like cells (3D amniogenesis) | 3 | Shao _et al_. Nature Mater 2017 | Shao _et al_. | H9_amnion_Shao |
| PRJNA276463 | RNA-Seq | CC2 Amnion_18_female | 1 | 18 gestational weeks | Roost _et al_. | amnion_18wk |
| PRJNA276463 | RNA-Seq | CJ1 Amnion_9_male | 2 | 9 gestational weeks | Roost _et al_. | amnion_9wk |
| PRJNA276463 | RNA-Seq | CI1 Amnion_16_male | 2 | 16 gestational weeks | Roost _et al_. | amnion_16wk |
| PRJNA276463 | RNA-Seq | CR1 Amnion_22_male | 2 | 22 gestational weeks | Roost _et al_. | amnion_22wk |
| PRJNA316992 | RNA-Seq | Term Amnion (Cont2,3,4,4b,6,7,8,9,11,12,14,15 RNA-seq) | 12 | Term fetal amnion | Suzuki _et al_. | amnion_term |
| PRJNA414247 | RNA-Seq | undifferentiated hESC line H9 cells | 2 | untreated | Krendl _et al_. | H9_Krendl |
| PRJNA414247 | RNA-Seq | hESC line H9 cells after 8 hours of BMP4 treatment | 2 | BMP4 exposed H9 cells | Krendl _et al_. | H9_BMP4_8h_Krendl |
| PRJNA414247 | RNA-Seq | hESC line H9 cells after 16 hours of BMP4 treatment | 2 | BMP4 exposed H9 cells | Krendl _et al_. | H9_BMP4_16h_Krendl |
| PRJNA414247 | RNA-Seq | hESC line H9 cells after 24 hours of BMP4 treatment | 2 | BMP4 exposed H9 cells | Krendl _et al_. | H9_BMP4_D1_Krendl |
| PRJNA414247 | RNA-Seq | hESC line H9 cells after 48 hours of BMP4 treatment | 2 | BMP4 exposed H9 cells | Krendl _et al_. | H9_BMP4_D2_Krendl |
| PRJNA414247 | RNA-Seq | hESC line H9 cells after 72 hours of BMP4 treatment | 2 | BMP4 exposed H9 cells | Krendl _et al_. | H9_BMP4_D3_Krendl |
| PRJNA720858 | snRNA-Seq | H1 ESC-derived TB_BAP D8 (20% O2)_snRNA-seq | 2 | BAP treatment | Khan _et al_. | H1_BAP_D8_20pcO2_Khan |
| PRJNA720858 | snRNA-Seq | H1 ESC-derived TB_BAP D8 (5% O2)_snRNA-seq | 2 | BAP treatment | Khan _et al_. | H1_BAP_D8_5pcO2_Khan |
| PRJNA705594 | scRNA-Seq | Naïve H9 ESC-derived nTE_D2 | 1 | ABPJ treatment | Io _et al_. | H9_sc.nTE_D2_Io |
| PRJNA705594 | scRNA-Seq | Naïve H9 ESC-derived nTE_D3 | 1 | ABPJ treatment | Io _et al_. | H9_sc.nTE_D3_Io |
| PRJNA705594 | scRNA-Seq | Naïve H9 ESC-derived nCT_D5 | 1 | ACE treatment | Io _et al_. | H9_sc.nCT_D5_Io |
| PRJNA705594 | scRNA-Seq | Naïve H9 ESC-derived nCT_D10 | 1 | ACE treatment | Io _et al_. | H9_sc.nCT_D10_Io |
## Other datasets
Custom [`PlacentaCellEnrich`](https://placentacellenrich.gdcb.iastate.edu/) were generated using:
1. [Xiang _et. al._](https://pubmed.ncbi.nlm.nih.gov/31830756/) dataset (NCBI BioProject:[PRJNA562548](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562548)).
2. [Castel _et al.,_](https://pubmed.ncbi.nlm.nih.gov/33238118/) publication, using data from [Petropoulos _et al.,_](https://pubmed.ncbi.nlm.nih.gov/27062923/) and [Zhou _et al.,_](https://pubmed.ncbi.nlm.nih.gov/31435013/) downloaded from [BitBucket](https://gitlab.univ-nantes.fr/E137833T/Castel_et_al_2020).