Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A temporal extracellular transcriptome atlas of human preimplantation development

ABSTRACT: A temporal extracellular transcriptome atlas of human preimplantation development

PROVIDER: PRJNA945056 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

A temporal extracellular transcriptome atlas of human preimplantation development

Project description:We develop a non-invasive method for comprehensive characterization of the extracellular RNAs (exRNA) in a single droplet of spent media that was used to culture human in vitro fertilization (IVF) embryos. We generate and provide as a resource the temporal extracellular transcriptome atlas of human preimplantation development (TETA). TETA consists of 245 exRNA sequencing datasets, corresponding to 245 collections of spent media at five developmental stages.

2023-11-14 | GSE227442 | GEO

An atlas of small non-coding RNAs in Human Preimplantation Development

Project description:An atlas of small non-coding RNAs in Human Preimplantation Development

| PRJNA1050210 | ENA

Single-cell identification of L1HS-Ta retrotransposons in preimplantation embryos by ATLAS-seq

Project description:We used ATLAS-seq to comprehensively map the genomic location of LINE-1 elements belonging to the youngest and potentially polymorphic subfamily (L1HS-Ta). This was performed in single-cells of 2 preimplantation embryos (E3 and E6) as well as from the remaining inner cell mass (denoted T). In brief, single cells were isolated from the inner cell mass of preimplantation embryos by laser drilling and micromanipulation. Whole-genome Multiple Displacement Amplification was performed on each isolated single cells, as well as on the remaining cells of the inner cell mass as a population (samples labelled 'T'). Then we applied ATLAS-seq to map L1HS-Ta retrotransposons. This approach relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of L1HS-Ta element junctions, and Ion Torrent sequencing using single-end 400 bp read chemistry. A notable aspect of ATLAS-seq is that we can obtain both L1 downstream and upstream junctions (3'- and 5'-ATLAS-seq libraries, respectively), for full-length L1 elements.

2023-09-30 | E-MTAB-8616 | biostudies-arrayexpress

An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]

Project description:An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]

| PRJNA1050220 | ENA

An atlas of small non-coding RNAs in Human Preimplantation Development [RNA-seq]

Project description:An atlas of small non-coding RNAs in Human Preimplantation Development [RNA-seq]

| PRJNA1049378 | ENA

Transcriptome of mouse preimplantation development

Project description:Transcriptome of mouse preimplantation development

| PRJNA291206 | ENA

An atlas of small non-coding RNAs in Human Preimplantation Development (Mouse embryo RNA-seq)

Project description:An atlas of small non-coding RNAs in Human Preimplantation Development (Mouse embryo RNA-seq)

| PRJNA1138744 | ENA

Transcription profiling of preimplantation mouse embryo development

Project description:Preimplantation mouse embryo development study on Affymetrix MOE430A. Zeng et al (2004) Dev Biol 272:483-496.

2008-06-11 | E-GEOD-1744 | biostudies-arrayexpress

Preimplantation mouse embryo development MOE430B

Project description:Preimplantation mouse embryo development on Affymetrix MOE430B. Zeng et al (2004) Dev Biol 272:483-496. Keywords: other

2004-09-10 | GSE1745 | GEO

An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]

Project description:Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency. Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.

2024-09-06 | GSE249708 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data