Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle


ABSTRACT: The experiment was designed to investigate transcriptional dynamics during definitive endoderm differentiation of human embryonic stem cells (hESCs) in early G1 phase of the cell cycle. For this, the FUCCI system was used to sort hESCs in Early G1 (EG1). Samples were taken at 0h (hESCs), 12h, 24h, 36h, 48h, 60h and 72h in triplicates. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) and residual genomic DNA was removed using the On-Column DNase I Digestion Set (Sigma-Aldrich) following manufacturer’s instructions. The libraries were generated at a library fragment size between 100 bp to 1 kb with Stranded RNAseq Standard with Oligo dT pulldown. All samples were amplified with a standard 10 PCR cycle before sequencing. The samples were multiplexed and analysed by Illumina Hiseq V4 with a paired end read-length PE75. RNA-seq data analysis was performed following recommendations described in Conesa et al. (DOI https://doi.org/10.1186/s13059-016-0881-8).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Siim Pauklin 

PROVIDER: E-MTAB-9194 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation.

Madrigal Pedro P   Deng Siwei S   Feng Yuliang Y   Militi Stefania S   Goh Kim Jee KJ   Nibhani Reshma R   Grandy Rodrigo R   Osnato Anna A   Ortmann Daniel D   Brown Stephanie S   Pauklin Siim S  

Nature communications 20230125 1


Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions lea  ...[more]

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