Niakan lab

Welcome to our Resources page; a space where you’ll find materials to support research in the field. Here, we share a curated collection of protocols, code, sequencing data, imaging data and more. You may use this resources freely to replicate experiments or explore our data, but please do not forget to acknowledge us!

Shiny App

Follow the link to explore our Shiny App: https://shiny.crick.ac.uk/embryo_signalling/

Expression browser: https://expression.niakan-lab.uk

GEO and EMBL-EBI ArrayExpress sequencing data

Study	Accession number
1. Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst (mouse)	GSE297478
2. Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst (human)	GSE297052, GSE250614, GSE250613, GSE239843
3. PBAT sequencing of human embryonic stem cells	EGAD50000001475
4. Investigating the role of NODAL signalling in preimplantation human embryos	GSE244736
5. IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche	GSE126488
6. Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos	PRJNA637030
7. Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing	GSE100120
8. Genome editing reveals a role for OCT4 in human preimplantation development [MiSeq]	GSE100119
9. Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing [RNA-seq]	GSE100118
10. KLF17 promotes human naïve pluripotency but is not required for its establishment [RNAseq]	E-MTAB-10958, E-MTAB-10915, E-MTAB-10914
11. Towards therapeutic application of pronuclear transfer to prevent transmission of mitochondrial DNA disease[scRNAseq]	GSE76284
12. Single-Cell RNA-seq Defines the Three Cell Lineages of the Human Blastocyst [scRNAseq]	GSE66507
13. Defining the three cell lineages of the human blastocyst by single-cell RNA-seq [box plots processed data]	Figshare: 1521657
14. Trophectoderm microdissected from human blastocysts cultured to day 5, day 6 and day 7 post-fertilisation [RNAseq]	E-MTAB-10749
15. Induced trophoblast stem cells reprogrammed from human embryonic stem cells [RNAseq]	E-MTAB-10748
16. Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells	GSE69323
17. Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells [ChIP-Seq & RNA-Seq]	GSE69322
18. Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells [time-course microarray]	GSE69321
19. Conversion of mES to cXEN cells	GSE38477
20. Gene Expression Analysis of Sox17-induced Mouse Embryonic Stem Cells [microarray]	GSE19028
21. Genome-Wide Sox17 Binding Sites in Mouse Extraembryonic Endoderm and Embryonic Stem Cells [ChIPseq]	GSE19026
22. Base editing reveals an essential role for NANOG in human embryogenesis [Raw embryo scRNAseq and hESC RNAseq]	GSE312160, GSE312763, GSE319780
23. Base editing reveals an essential role for NANOG in human embryogenesis [Sequence Read Archive (SRA) database accession number]	PRJNA1431218
24. Human Naïve-to-Primed Epiblast Transition Requires Suppression of Extraembryonic Competence by SALL2 [All raw fastq files]	PRJNA1439293
25. Human Naïve-to-Primed Epiblast Transition Requires Suppression of Extraembryonic Competence by SALL2 [CUT&Tag for SALL2 binding] [RNA-seq for E8 priming in SALL2-/-] [RNA-seq for signalling perturbation in SALL2-/-] [scATAC-seq for SALL2-/-] [scRNA-seq for SALL2-/-]	GSE325560 GSE325561 GSE325562 GSE325563 GSE325564

Other sequencing data

1. Base editing reveals an essential role for NANOG in human embryogenesis [Low-pass whole genome sequencing mapped datasets]

Imaging data

• Live imaging of late-stage preimplantation human embryos reveals late-stage de novo mitotic errors [light sheet imaging data]: https://doi.org/10.5281/zenodo.16996800, https://doi.org/10.5281/zenodo.16994339 and https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD2325?query=%20S-BIAD2325
• Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [confocal imaging data]: https://figshare.com/articles/dataset/Suppression_of_ERK_signalling_promotes_pluripotent_epiblast_in_the_human_blastocyst/28597145
• NODAL signalling does not initiate or maintain the pluripotent epiblast in pre-implantation human development [confocal imaging data BioImage Archive]: S-BIAD1398
• 3 CSV files below related to the study “Live imaging of late-stage preimplantation human embryos reveals de novo mitotic errors” for lineage tracing across the three embryos. The CSV files include annotated time, cellID, parentID, X, Y, Z coordinates.

• Human embryo immunofluorescence data from the manuscript: Base editing reveals an essential role for NANOG in human embryogenesis.

Github & Zenodo

1. Segmentation and image analysis pipeline for the investigation of NODAL signalling in early human development (confocal image segmentation and analysis): https://doi.org/10.25418/crick.19383428.v1
2. Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst (confocal image segmentation and analysis): https://zenodo.org/records/15640446
3. Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst (Single cell RNAseq analysis and mapped data): https://zenodo.org/records/15128175 https://github.com/brickmanlab/simon-et-al-2024
4. MICA: a multi-omics method to predict gene regulatory networks in early human embryos (data processing and analysis scripts): https://github.com/galanisl/early_hs_embryo_GRNs
5. Frequent loss-of-heterozygosity in CRISPR-Cas9–edited early human embryos (data processing and analysis scripts): https://github.com/galanisl/loh_scripts
6. Initiation of a conserved trophectoderm program in human, cow and mouse embryos (data processing and analysis scripts): https://github.com/galanisl/TE_differentiation
7. IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche (data processing and analysis scripts): https://github.com/galanisl/AI_hESCs
8. Human Naïve-to-Primed Epiblast Transition Requires Suppression of Extraembryonic Competence by SALL2: https://github.com/Qiulin-Huang/Niakan-lab-public

Plasmids

Follow the link to explore the materials the Niakan Lab has deposited at Addgene: http://www.addgene.org/Kathy_Niakan. Find a summary table below.

Study	Plasmid ID
Base editing reveals an essential role for NANOG in human embryogenesis	259160 CAG Promoter-Driven ABE8e-dCas9-NG 259161 CAG Promoter-Driven ABE8e-dCas9

Protocols

Virus production & Transduction

Cell culture protocols

Embryo protocols

Imaging protocols