Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens, XX) |
RUES2 | US National Institutes of Health, human ESC registry | human ESC registry no. 0013; RRID:CVCL_VM29 | Human embryonic stem cell line |
| Cell line (Homo sapiens, XX) |
RUES2-RFP-SMAD1 | this paper | CRISPR/Cas9-modified human embryonic stem cell line |
|
| Cell line (Homo sapiens, XX) |
RUES2-mCit-SMAD2 | this paper | CRISPR/Cas9-modified human embryonic stem cell line |
|
| Cell line (Homo sapiens, XX) |
RUES2-GFP-SMAD4 | PMID: 28760810 | CRISPR/Cas9-modified human embryonic stem cell line |
|
| Cell line (Homo sapiens, XX) |
RUES2-SMAD3-/- clone #1 | this paper | CRISPR/Cas9-modified human embryonic stem cell line |
|
| Cell line (Homo sapiens, XX) |
RUES2-SMAD3-/- clone #2 | this paper | CRISPR/Cas9-modified human embryonic stem cell line |
|
| Cell line (Homo sapiens, XY) |
RUES1 | US National Institutes of Health, human ESC registry | human ESC registry no. 0012; RRID:CVCL_B809 |
Human embryonic stem cell line |
| Antibody | anti-Brachyury (goat polyAb) |
R and D Systems | Cat. #: AF2085; RRID:AB_2200235 |
IF (1:300) |
| Antibody | anti-Brachyury (rabbit mAb) |
R and D Systems | Cat. #: MAB20851 | IF (1:200) |
| Antibody | anti-Cdx2 (mouse mAb) |
Abcam | Cat. #: ab15258; RRID:AB_2077042 |
IF (1:50) |
| Antibody | anti-Eomes (mouse mAb) |
R and D Systems | Cat. #: MAB6166; RRID:AB_10919889 |
IF (1:200) |
| Antibody | anti-Lamin B1 (rabbit polyAb) |
Proteintech | Cat. #: 12987–1-AP; RRID:AB_2136290 |
WB (1:2000) |
| Antibody | anti-Goosecoid (goat polyAb) |
R and D Systems | Cat. #: AF4086; RRID:AB_2114650 |
IF (1:100) |
| Antibody | anti-Nanog (goat polyAb) |
R and D Systems | Cat. #: AF1997; RRID:AB_355097 |
IF (1:200) |
| Antibody | anti-Oct3/4 (mouse mAb) |
BD Biosciences | Cat. #: 611203; RRID:AB_398737 |
IF (1:400) |
| Antibody | anti-Smad2 (rabbit mAb) |
Cell Signaling | Cat. #: 3122; RRID:AB_10697649 |
IF (1:200), WB (1:1000) |
| Antibody | anti-Smad2/3 (mouse mAb) |
BD Biosciences | Cat. #: 610842; RRID:AB_398161 |
IF (1:100) |
| Antibody | anti-Sox17 (goat polyAb) |
R and D Systems | Cat. #: AF1924; RRID:AB_355060 |
IF (1:200) |
| Antibody | anti-Sox2 (rabbit mAb) |
Cell Signaling | Cat. #: 3579; RRID:AB_2195767 |
IF (1:200) |
| Peptide, recombinant protein |
recombinant human/mouse/ rat Activin A |
R and D Systems | Cat. #: 338-AC/CF | |
| Peptide, recombinant protein |
recombinant human BMP-4 |
R and D Systems | Cat. #: 314 BP | |
| Peptide, recombinant protein |
recombinant mouse Wnt-3a |
R and D Systems | Cat. #: 1324-WN | |
| Peptide, recombinant protein |
recombinant human Laminin-521 |
BioLamina | ||
| Chemical compound, drug |
endo-IWR-1 | Tocris | Cat. #: 3532 | |
| Chemical compound, drug |
IWP-2 | Stemgent | Cat. #: 04–0034 | |
| Chemical compound, drug |
SB431542 | Stemgent | Cat. #: 04–0010 | |
| Chemical compound, drug |
Y-27632 | Abcam | Cat. #: Ab120129 | |
| Software, algorithm |
MATLAB | MathWorks | RRID:SCR_001622 | |
| Software, algorithm |
StemCellTracker | https://github.com/ChristophKirst/StemCellTracker | Image segmentation and signal analysis |
|
| Software, algorithm |
R | https://www.r-project.org/ | ||
| Software, algorithm |
DESeq2 Bioconductor package |
PMID: 25516281 | Differential gene expression analysis |
|
| Software, algorithm |
PWMEnrich Bioconductor package |
https://bioconductor.org/packages/release/bioc/html/PWMEnrich.html | Motif enrichment analysis | |
| Software, algorithm |
GOseq Bioconductor package |
PMID: 20132535 | Statistical analysis of over/under represented categories |
|
| Software, algorithm |
AME | PMID: 25953851 | Motif enrichment analysis |
|
| Software, algorithm |
Tide | PMID: 25300484 | Sequence trace decomposition |
|
| Software, algorithm |
Cluster 3.0 | PMID: 14871861 | Clustering | |
| Software, algorithm |
Java TreeView | PMID: 15180930 | Data visualization |