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| Status |
Public on Jun 25, 2024 |
| Title |
BirthSeq, a new method to isolate and analyze dated cells in different vertebrates |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well-documented, with evidence showing that time plays a critical role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via FACS, and analysis using high-throughput techniques. We tuned up BirthSeq in developmental organs across three vertebrate species (mouse, chick, and gecko), and fully made use of it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organism, helping to fill the necessity in developmental biology research by targeting cells and their temporal cues.
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| Overall design |
Single cell RNA sequencing of birthdated cells from chicken and mouse were obtained by Birth-seq protocol published in this article. Birthdated cells with fluorescence EdU were FAC-Sorted and then droplet captured with 10X Genomics Chronium V3 pipeline. Libraries were sequenced with Novaseq 6000 for 50000 reads.
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| Contributor(s) |
Rueda-Alaña E, Grillo M, Vázquez E, Marco-Salas S, Senovilla-Ganzo R, Escobar L, Quintas-Gorozarri A, Benguría A, Aransay AM, Bengoa-Vergniory N, Dopazo A, Encinas JM, Nilson M, García-Moreno F |
| Citation missing |
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| Submission date |
Jun 20, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Fernando García-Moreno |
| E-mail(s) |
fernando.garcia-moreno@achucarro.org
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| Organization name |
Achucarro BCN
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| Street address |
Barrio Sarriena s/n Edificio Sede
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| City |
Leioa |
| State/province |
Bizkaia |
| ZIP/Postal code |
48940 |
| Country |
Spain |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1126123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE270283_Mouse_Day2_NeuralCells_Named_Subclustering.rds.gz |
388.3 Mb |
(ftp)(http) |
RDS |
| GSE270283_RAW.tar |
261.3 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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