Timecourse single-cell RNA-seq of whole rabbit embryos sampled across gestational days 7, 8 and 9

Experiment ID:ERP139683
Technology:scRNA-Seq
Description:We characterised the transcriptomic profiles of 146,133 individual cells (post-QC) from whole rabbit embryos spanning gestational days 7, 8 and 9. These experiments were performed to elucidate the molecular programmes underlying gastrulation and early organogenesis in a non-rodent mammal. Combined with existing datasets of early mouse development, our rabbit developmental atlas facilitates a broad cross-species approach to deciphering early human development. Cell libraries were prepared using the 10X Genomics Chromium platform.
DOI:10.1038/s41556-023-01174-0
Source:ERP139683 ENA
Download:
scRNA-Seq droplet-based processed expression values per cell population in Oryctolagus cuniculusscRNA-Seq droplet-based H5AD data per cell in Oryctolagus cuniculus

List of assays

Show

entries

Showing 1 to 20 of 602 entries

Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX9511921CL:0000352 epiblast cellEpiblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967017451582430118258Browse results
ERX9511921CL:0000349 extraembryonic cellAllantois endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967013779964814131Browse results
ERX9511921CL:0000223 endodermal cellDefinitive EndodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28589742718581196701659420212309.5Browse results
ERX9511921CL:0002323 amniocyteAmnion 1UBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967010959550513579Browse results
ERX9511921CL:0000523 mononuclear cytotrophoblast cellCytotrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967016462366014238.5Browse results
ERX9511921CL:0011026 progenitor cellCardiopharyngeal progenitorsUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28589742718581196703649635612838Browse results
ERX9511921CL:0000115 endothelial cellEmbryo proper endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967028191186114715Browse results
ERX9511921CL:0002321 embryonic cellAnterior Primitive StreakUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28589742718581196704160736261917285.5Browse results
ERX9511921CL:0000221 ectodermal cellPlacodal ectodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28589742718581196709296850813691.5Browse results
ERX9511921CL:0011010 lateral mesodermal cellLateral plate mesodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2858974271858119670815613411710Browse results
ERX9511921CL:0000351 trophoblast cellTrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967010038459316817469Browse results
ERX9511921CL:0000222 mesodermal cellNascent mesodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28589742718581196707588350322317584Browse results
ERX9511921CL:0000670 primordial germ cellPGCUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired285897427185811967029907084615292Browse results
ERX9511922CL:0000352 epiblast cellEpiblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired850323225565469512028220850548318643Browse results
ERX9511922CL:0000349 extraembryonic cellAllantois endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired8503232255654695120369450105314886Browse results
ERX9511922CL:0000223 endodermal cellDefinitive EndodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired85032322556546951201777625198516769.5Browse results
ERX9511922CL:0002323 amniocyteAmnion 1UBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired850323225565469512016932461613935Browse results
ERX9511922CL:0000523 mononuclear cytotrophoblast cellCytotrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired8503232255654695120755612139315707Browse results
ERX9511922CL:0011026 progenitor cellEMPUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired85032322556546951206533545813324.5Browse results
ERX9511922CL:0000115 endothelial cellEmbryo proper endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired85032322556546951208959557613678.5Browse results

Showing 1 to 20 of 602 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again