README

BAPvsTrophoblast_Amnion

Tuteja Lab, 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 here on GitHub.

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 were generated using:

  1. Xiang et. al. dataset (NCBI BioProject:PRJNA562548).
  2. Castel et al., publication, using data from Petropoulos et al., and Zhou et al., downloaded from BitBucket.