4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA765361 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16013023.fastq.gz | Fastqsanger.gz | |||
| SRR16013024.fastq.gz | Fastqsanger.gz | |||
| SRR16013025.fastq.gz | Fastqsanger.gz | |||
| SRR16013026.fastq.gz | Fastqsanger.gz | |||
| SRR16013027.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body
| PRJNA770075 | ENA
Project description:4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body
| PRJNA765362 | ENA
Project description:Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility. ### Competing Interest Statement The authors have declared no competing interest.
2021-10-11 | GSE185608 | GEO
Project description:Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility. ### Competing Interest Statement The authors have declared no competing interest.
2021-09-24 | GSE184602 | GEO
Project description:Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility. ### Competing Interest Statement The authors have declared no competing interest.
2021-09-24 | GSE184600 | GEO
Project description:mESCs were in vitro differentiated into embryoid bodies under suspension cultured condition and was collected at day 9 of differentiation. Polyadenylated mRNAs of mESCs and EBs were isolated and used to build the sequencing library.
2024-08-23 | GSE226212 | GEO
Project description:Embryonic stem (ES) cells, when grown in suspension culture without feeders, spontaneously form round structures known as embryoid bodies. Given the appropriate conditions, these cells can differentiate over time into precursors of all three germ layers. Embryoid bodies, in a disorganized way, mimic early embryonic development to a certain extent and can be used as a synchronously differentiating large scale source of tissue for the study of biological determinants of early differentiation. Embryoid bodies have been used as a source for most early protocols that derive specific differentiated cell types from undifferentiated ES cells, although some protocols, notably those that derive neurons from ES cells, have moved on from EBs as a result of varying replicability and yield. We have decided to look at the transcriptomic profiles of embryoid bodies during the initial stages of embryoid body formation and differentiation, in order to pinpoint novel determinants of key developmental stages. Keywords: time course
2007-08-15 | GSE8766 | GEO
Project description:V6.5 mESCs over-expressing V5-tagged Csrp1 and wild-type mESCs were differentiated into embryoid bodies (EBs) and collected at day 9 for CLIP-seq.
2024-08-23 | GSE226213 | GEO
Project description:Human pluripotent stem cells were differentiated by size-controlled embryoid body (EB) formation in defined neutral, ectoderm, endoderm and mesoderm conditions. EB's were analysed at 4, 10 and 16 days post induction by real-time PCR using the Fludigm Deltagene primers and probes.
2017-06-20 | GSE97963 | GEO
Project description:Mouse WT129 ESCs were differentiated into glutamatergic neurons and samples were collected at days 0 (mESCs), 4 (embryoid bodies), 8 (neuronal precursors) and 12 (neurons). These are RNA-seq data to profile RNA expression during differentiation.
2020-05-21 | E-MTAB-8197 | biostudies-arrayexpress