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
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scRNA-Seq droplet-based processed expression values per cell population in Oryctolagus cuniculusscRNA-Seq droplet-based H5AD data per cell in Oryctolagus cuniculus

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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
ERX9511924CL:0000352 epiblast cellEpiblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533507359443316817710.5Browse results
ERX9511924CL:0000223 endodermal cellDefinitive EndodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired1636267251096053350704628120916027Browse results
ERX9511924CL:0002323 amniocyteAmnion 1UBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired163626725109605335027359671414321Browse results
ERX9511924CL:0000523 mononuclear cytotrophoblast cellCytotrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533502609126512363Browse results
ERX9511924CL:0011026 progenitor cellHaematoendothelial progenitorsUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533501567799173216295Browse results
ERX9511924CL:0000115 endothelial cellEmbryo proper endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533502835829712659Browse results
ERX9511924CL:0002321 embryonic cellAnterior Primitive StreakUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533501511978173716491Browse results
ERX9511924CL:0000351 trophoblast cellTrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533505889011249116946Browse results
ERX9511924CL:0000222 mesodermal cellNascent mesodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533502492048209016748Browse results
ERX9511924CL:0000670 primordial germ cellPGCUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533509441047914105.5Browse results
ERX9511924CL:0007005 notochordal cellNotochordUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired16362672510960533506253637913769.5Browse results
ERX9511925CL:0000352 epiblast cellEpiblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired271067730174528590015124636402118123.5Browse results
ERX9511925CL:0000349 extraembryonic cellAllantois endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2710677301745285900600940113415328Browse results
ERX9511925CL:0000223 endodermal cellDefinitive EndodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired27106773017452859001240613146616295Browse results
ERX9511925CL:0002323 amniocyteAmnion 1UBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired271067730174528590014820558913832.5Browse results
ERX9511925CL:0000523 mononuclear cytotrophoblast cellCytotrophoblastUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired27106773017452859002673883202516646Browse results
ERX9511925CL:0011026 progenitor cellCardiopharyngeal progenitorsUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired27106773017452859009207550113650.5Browse results
ERX9511925CL:0000115 endothelial cellEmbryo proper endotheliumUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2710677301745285900596191112415330.5Browse results
ERX9511925CL:0002321 embryonic cellAnterior Primitive StreakUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired27106773017452859004737463267817290.5Browse results
ERX9511925CL:0000221 ectodermal cellPlacodal ectodermUBERON:0004716 conceptuswhole organismUBERON:0000068 embryo stagegestational day 7mixedNew Zealand white rabbitNANAOryctolagus cuniculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired271067730174528590010655756213908.5Browse results

Showing 41 to 60 of 602 entries

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