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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 20, 2022 |
| Title |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We have developed a novel in vitro protocol for the derivation of bona fide Pharyngeal Endoderm (PE) cells from hESCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone marks.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| Contributor(s) |
Cipriano A, Colantoni A, Calicchio A, Fiorentino J, Gomes D, Moqri M, Parker A, Rasouli S, Caldwell M, Briganti F, Roncarolo MG, Baldini A, Weinacht KG, Tartaglia GG, Sebastiano V |
| Citation(s) |
39118163 |
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| Submission date |
Jul 15, 2022 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Alessio Colantoni |
| E-mail(s) |
alessio.colantoni@uniroma1.it
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| Organization name |
"Sapienza" University of Rome
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| Department |
Dipartimento di Biologia e Biotecnologie "Charles Darwin"
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| Lab |
Tartaglia Lab
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| Street address |
Piazzale Aldo Moro, 5
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| City |
Roma |
| State/province |
RM |
| ZIP/Postal code |
00185 |
| Country |
Italy |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (50)
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| GSM6256946 |
ChIP DE H3K27me3, replicate B |
| GSM6256947 |
ChIP DE H3K4me1, replicate A |
| GSM6256948 |
ChIP DE H3K4me1, replicate B |
| GSM6256949 |
ChIP DE H3K4me3, replicate A |
| GSM6256950 |
ChIP DE H3K4me3, replicate B |
| GSM6256951 |
ChIP DE Input, replicate A |
| GSM6256952 |
ChIP DE Input, replicate B |
| GSM6256953 |
ChIP PE H3K27ac, replicate A |
| GSM6256954 |
ChIP PE H3K27ac, replicate B |
| GSM6256955 |
ChIP PE H3K27me3, replicate A |
| GSM6256956 |
ChIP PE H3K27me3, replicate B |
| GSM6256957 |
ChIP PE H3K4me1, replicate A |
| GSM6256958 |
ChIP PE H3K4me1, replicate B |
| GSM6256959 |
ChIP PE H3K4me3, replicate A |
| GSM6256960 |
ChIP PE H3K4me3, replicate B |
| GSM6256961 |
ChIP PE Input, replicate A |
| GSM6256962 |
ChIP PE Input, replicate B |
| GSM6256963 |
ChIP PE Input for H3K4Me1, replicate A |
| GSM6256964 |
ChIP PE Input for H3K4Me1, replicate B |
| GSM6256965 |
BulkRNA hESCs, replicate A |
| GSM6256966 |
BulkRNA hESCs, replicate B |
| GSM6256967 |
BulkRNA hESCs, replicate C |
| GSM6256968 |
BulkRNA DE, replicate A |
| GSM6256969 |
BulkRNA DE, replicate B |
| GSM6256970 |
BulkRNA DE, replicate C |
| GSM6256971 |
BulkRNA AFE, replicate A |
| GSM6256972 |
BulkRNA AFE, replicate B |
| GSM6256973 |
BulkRNA AFE, replicate C |
| GSM6256974 |
BulkRNA PE, replicate A |
| GSM6256975 |
BulkRNA PE, replicate B |
| GSM6256976 |
BulkRNA PE, replicate C |
| GSM6256977 |
ATAC DE, replicate A |
| GSM6256978 |
ATAC DE, replicate B |
| GSM6256979 |
ATAC AFE, replicate A |
| GSM6256980 |
ATAC AFE, replicate B |
| GSM6256981 |
ATAC PE, replicate A |
| GSM6256982 |
ATAC PE, replicate B |
| GSM6340943 |
scRNA DE |
| GSM6340944 |
scRNA PE |
| GSM8384902 |
ChIP AFE RARα IP |
| GSM8384903 |
ChIP AFE RARα Input |
| GSM8384904 |
ChIP PE RARα IP |
| GSM8384905 |
ChIP PE RARα Input |
| GSM8444007 |
scRNA DE (Day 2), Batch_2 |
| GSM8444008 |
scRNA AFE (Day 3), Batch_2 |
| GSM8444009 |
scRNA AFE (Day 5), Batch_2 |
| GSM8444010 |
scRNA PE (Day 5 + RA), Batch_2 |
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| This SuperSeries is composed of the following SubSeries:
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| GSE206566 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Histone Modification ChIP-Seq) |
| GSE206567 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Bulk RNA-Seq) |
| GSE206568 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (ATAC-Seq) |
| GSE208317 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Single-cell RNA-Seq) |
| GSE271773 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (RARα ChIP-Seq) |
| GSE274133 |
Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Single-cell RNA-Seq Batch_2) |
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| Relations |
| BioProject |
PRJNA859177 |
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