PGP cells and Omic resources

NIST-FDA Genome in a Bottle Authoritative Characterization of Benchmark Human Genomes.

Papers on PGP1 Synthetic biology: CRISPR, Epigenetic programming.

491. Musah S, Dimitrakakis N, Camacho DM, Church GM, Ingber DE (2018) Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip. Nat Protoc. 13(7):1662-1685. PMID: 29995874

462s. Yankner B, et al. (2018). Inhibitory neurons [in prep]

461s. Khoshakhlagh P,  Ng AHM, et al. (2018)  Oligodendrocytes. [in prep]

460s.  Ng AHM, Khoshakhlagh P, Shipman S, Swiersy A, Appleton E, Huang J, Saylor W, Trono D, Taipale J, Hill D, Vidal M, Busskamp V, Church GM (2018) Programming cell fates using a comprehensive human transcription factor library. [submitted. -- using PGP1 iPSCs to characterize a comprehensive set of 1,748  human transcription factor open reading frames in expression clones,  at least 204 of which drove stem cells into diverse cellular states.  Some cell states require multiple TFs, which we determine from transcriptomes of the target cells guiding combinatorial screens.]

400. Musah S, Mammoto T, Mammoto A, Ferrente TC, Hirano-Kobayashi M, Roberts K, Chung S, Novak R, Ingram M, Fatanat-Didar T, Weaver JC, Church GM, Ingber DE (2017) Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip. Nat Biomed Eng. PMID: 29038743

350. Yang L, Grishin D, Zhang CZ, Wang G, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G (2014) Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nature Comm. 5:5507. PMID: 25425480

344. Yang L, Yang JL, Byrne S, Pan J, Church GM (2014) CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol. 107:31.1.1-31.1.17. PMID: 24984853

312. Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT. (2014) Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nature Medicine 20: 616-23.

297. Busskamp V, Lewis NE, Guye P, Ng AHM, Shipman S, Byrne SS, Sanjana NE, Li Y, Weiss R, Church GM (2014) Rapid neurogenesis through transcriptional activation in human stem cells. Molecular Systems Biology MSB 10:760: 1-21. PMID: 25403753

275. Yang L, Guell M, Byrne S, Yang J, De Los Angeles A, Mali P, Aach J, Briggs A, Rios X, Huang PY, Daley G, Church GM (2013). Optimization of Scarless Human Stem Cell Genome Editing. Nucleic Acids Res. PMID: 23907390

273. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville J, Church GM (2013) RNA-guided human genome engineering via Cas9. Science, Jan 3. 339(6121): 823-6. PMID: 23287722

466s. Smith CJ, Castanon O, Khoshakhlagh P, Güell M, Wang S, Said K, Yildiz R, Dysart M, Thompson D, Myllykallio H, Church GM (2018) Repeats. [in prep.]

Papers on PGP1 haplotyping & 3D structure: ENCODE Project Hi-C on 11 isogenic cell types (Erez Lieberman, et al.). HiC is helpful for long-range assembly.  Also using PGP1-iPSC for whole genome FISSEQ and Oligopaints at 20 nm resolution, which may yield full 3D structure including bridging current centromeric gaps.

474a. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K (2017) Ultraaccurate genome sequencing and haplotyping of single human cells PNAS 114(47):12512-12517. Suppl. Seq. data PMID: 29078313

464a.  Nir G, Farabella I, ... Wu CT (2018) Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. Biorxiv.

463a. Nguyen H, Wu CT, et al. (2018) Imaging [in prep.]

304. Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K (2013) On the design of clone-based haplotyping. Genome Biology 14(9):R100. PMID: 24028704 BAC Library (5X coverage).

247. Peters BA, et al.  (2012) Accurate whole genome sequencing and haplotyping from 10-20 human cells. Nature 487: 190-195. (supplement) PMID: 22785314

226a. Gore A, Li Z, Fung HL, Young J, Agarwal S, Antosiewicz-Bourget J, Canto I, Israel M, Kiskinis E, Lee JH, Loh YH, Manos P, Montserrat N, Wilbert M, Yu J, Kirkness E, Belmonte JCI, Daley GQ, Eggan K, Rossi DJ, Thomson J, Goldstein LSB, Zhang K (2011) Somatic coding mutations in human induced pluripotent stem cells. Nature 471, 63-67. PMID: 21368825

A key resource for absolute haplotyping (Maternal/Paternal) is half-sibling (on maternal side) who has public PGP SNPs and WGS data.

Papers on PGP1  RNA and other cellular phenotypes.

463s. Chan Y, Chan YK, Goodman DB, Chavez A, Lim ET, Church GM (2018) Multiplexed testing of pooled donor cells using SNPs and NGS. (in prep.)

342. Lee J, Daugharthy ER, Scheiman J, Kalhor R, Ferrente TC, Terry R, Turczyk B, Yang JL, Lee HS, Aach J, Zhang K, Church GM (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nature Protocols. PMID: 25675209

303. Lee J, Daugharthy E, Scheiman J, Kalhor R, Yang JL, Ferrente TC, Terry R, Jeanty SSF, Li C,Amamoto R, Peters DT, Turczyk BM, Marblestone A, Inverso S, Bernard A, Mali P, Rios X, Aach J, Church GM (2014) Highly multiplexed subcellular RNA sequencing in situ. Science 343(6177):1360-3. PMID: 24578530

253. Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden J, Kelton W, Jung ST, Liu Y, Laserson J, Chari R, Lee J, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein S, Church GM (2014) High-resolution antibody dynamics of vaccine-induced immune responses. PNAS 111(13):4928-33. PMID: 24639495

189. Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E, Eggan K, Church GM (2009) Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human. Nature Methods 6(8):613-8. PMID:19620972 PMC2742772

188. Lee J, Park IH, Gao Y, Li JB, Li Z, Daley G, Zhang K, Church GM (2009) A Robust Approach to Identifying Tissue-specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLoS Genetics 5(11):e1000718. PMID: 19911041 PMC2766639

Epigenetically distinct isogenic PGP1 cells in NIH ENCODE Project core analyses (ChIP-seq, RNA-Seq, DNA-mC, Hi-C) & Coriell (for #1,2,15)
Homogeneity % without purification, unless specified.

#1. Primary fibroblastsGM23248 100% [303][342]
#2. IPSCs (from #1 via retroviral Yamanaka factors)GM23338 100% [226]
#3. Bipolar neurons  (from #2 via NGN1/2)  >95% [292]
#4. IPSCs (from #1 via Sendai-viral Yamanka factors)  100%
#5. Lymphoblastoid cells (from primary B-cells at Coriell)  100%  [188][463]
#6. Other neuronal types (from #4)  >90-95% excitatory cortical neurons [297]
#7. Oligodendrocytes (from #4)  >70% oligodendrocytes - have surface markers for purification if needed [461]
#8. Endothelial cells (from #4)  >90% [460]
#9. Cardiomyocytes (from #4)   >90% after metabolic selection  [350]
#10. Myocytes (from #4)  >50% - we're still working on this
#11. Stromal cells (from #4)  >90% [460]
#12. Astrocytes  (from #4)   >90% - we're still characterizing this [460]
#13. Inhibitory multiprocess neurons (from #4) from Bruce Yankner [462]
#14. Keratinocytes, primary [189]
#15.  B-cells primary, GM20431 [253]

Full set of papers on PGP, the project: personalgenomes.org

Data on PGP1, the person: hu43860C

NIST-FDA Genome Editing Consortium.

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