BAPvsTrophoblast_Amnion

Tuteja Lab, Iowa State University, Ames IA-50011

The HTML version of this documentation is available here:

Documentation

1. Section 1: Preparing datasets for anlayses
2. Section 2: DESeq2 analyses
3. Section 3: PCA plots for the datasets
4. Section 4: Finding novel amnion markers
5. Section 5: sn/scRNAseq data analyses
6. Section 6: Custom encrichment dataset preparation

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
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
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
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

Syncytiotrophoblast (STB) genes expression were tested against Zhou et. al., dataset (GSE109555).

Custom PlacentaCellEnrich were generated using: Xiang et. al.(NCBI BioProject: PRJNA562548 and Castel et al. publication, using data from Petropoulos et al., and Zhou et al., downloaded from BitBucket

Contacts

1. Project related questions: Geetu Tuteja
2. Scripts and workflow related questions: please open an issue here on GitHub.

Publication

If you use the scripts from this repository in your research, please cite this publication:

Seetharam, Arun S., Ha TH Vu, Sehee Choi, Teka Khan, Megan A. Sheridan, Toshihiko Ezashi, R. Michael Roberts, and Geetu Tuteja. "The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion." Stem Cell Reports (2022). Available online 19 May 2022.