KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-α-actinin antibody | Sigma-Aldrich | Cat#: A7811; RRID: AB_476766 |
| Rat anti-ZO1 antibody | DSHB | Cat#: R26.4C; RRID: AB_2205518 |
| Rabbit anti-UPK1B antibody | Thermo Fisher Scientific | Cat#: PA5–72711; RRID: AB_2718565 |
| Alexa Fluor 488 Goat Anti-Rabbit IgG | Thermo Fisher Scientific | Cat#: A-11034; RRID: AB_2576217 |
| Alexa Fluor 555 Goat Anti-Mouse IgG | Thermo Fisher Scientific | Cat#: A-21422; RRID: AB_141822 |
| Alexa Fluor 647 Goat Anti-Rabbit IgG | Thermo Fisher Scientific | Cat#: A-21245; RRID: AB_2535813 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant human TGF-beta 1 protein | R&D Systems | Cat#: 240-B |
| Critical Commercial Assays | ||
| Aldefluor Kit | STEMCELL Technologies | Cat#: #01700 |
| Deposited Data | ||
| Raw reads | This paper | GEO: GSE117795 |
| Gene expression matrices | This paper | GEO: GSE117795 |
| Oligonucleotides | ||
| gcgcATCGATATGATGCTTCAACATCCAGGCCAG | This paper | Clal_Atf3_5 |
| gcgcGTCGACTTAGCTCTGCAATGTTCCTTCTTTTATCTGTTGG | This paper | Sall_Atf3_3 |
| gcgcATCGATATGCGGCGGTCGCC | This paper | Clal_Bnc1_5 |
| gcgcGTCGACTTACTGGAGGTGGCTTGGAGATGAAG | This paper | Sall_Bnc1_3 |
| gcgcATCGATATGTCCACTGGCTCCCTCAGC | This paper | Clal_Tcf21_5 |
| gcgcGTCGACTCAGGATGCTGTAGTTCCACACAAGC | This paper | Sall_Tcf21_3 |
| gcgcATCGATATGAGTCTGGTGGGGGGC | This paper | Clal_Hand2_5 |
| gcgcGAATTCTCACTGCTTGAGCTCCAGGG | This paper | EcoRl_Hand2_3 |
| gcgcgcCAATTGATGGCCTTGACTGACGGCGGC | This paper | Mfel_Gata6_5cds |
| gcgcgcCTCGAGTCAGGCCAGGGCCAGAGCAC | This paper | Xhol_Gata6_3cds |
| qPCR primers | This paper | Table S3 |
| Software and Algorithms | ||
| bcl2fastq (version 2.17.1.14) | Illumina | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html |
| Cell Ranger (version 2.1.0) | 10x Genomics | https://www.10xgenomics.com |
| Drop-seq Tools (version 1.12) | Macosko et al., (2015) | http://mccarrolllab.com/dropseq |
| featureCounts (version 1.5.3) | Liao et al., (2014) | http://bioinf.wehi.edu.au/featureCounts |
| Gviz (version 1.24.0) | Hahne and Ivanek, (2016) | https://bioconductor.org/packages/release/bioc/html/Gviz.html |
| irlba (version 2.3.2) | Jim Baglama, Lothar Reichel, B. W. Lewis | https://cran.r-project.org/web/packages/irlba/index.html |
| Monocle (version 2.8.0) | Qiu etal., (2017) | http://cole-trapnell-lab.github.io/monocle-release/ |
| R (version 3.5.1) | R Foundation | https://www.r-project.org |
| Rtsne (version 0.13) | van der Maaten, (2014) | https://cran.r-project.org/web/packages/Rtsne/index.html |
| SAMtools (version 1.8) | Li et al., (2009) | https://www.htslib.org |
| STAR (version 2.5.3a) | Dobin et al., (2013) | https://github.com/alexdobin/STAR |
| sva (version 3.28.0) | Johnson et al., (2007) | https://bioconductor.org/packages/release/bioc/html/sva.html |
| topGO (version 2.32.0) | Adrian Alexa, Jorg Rahnenfuhrer | https://bioconductor.org/packages/release/bioc/html/topGO.html |
| UMI-tools (version 0.5.3) | Smith etal., (2017) | https://github.com/CGATOxford/UMI-tools |
| org.Mm.eg.db (version 3.4.1) | Marc Carlson | https://bioconductor.org/packages/release/data/annotation/html/org.Mm.eg.db.html |
| GO.db (version 3.4.1) | Marc Carlson | https://bioconductor.org/packages/release/data/annotation/html/GO.db.html |
| igraph (version 1.2.1) | https://cran.r-project.org/web/packages/igraph/AUTHORS | https://igraph.org/ |
| RANN (version 2.6) | Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis | https://cran.r-project.org/web/packages/RANN/index.html |
| Code for this manuscript | This paper | https://github.com/jlduan/Reprogram-Seq |
| Other | ||
| Medium 199 | GIBCO | Cat#: 11150059 |
| Fetal bovine serum | Sigma-Aldrich | Cat#: F6178/F0926 |
| GlutaMAX | GIBCO | Cat#: 35050061 |