Table · dataset · 2025
Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles
Listed in Edmond
Single-cell RNA-seq datasets from turtle and lizard samples, provided as Seurat objects in both .Robj and .h5seurat formats.
Description
Each dataset includes the raw gene–cell count matrix, cell and gene metadata, normalized and batch-corrected data, PCA and t-SNE embeddings, and cluster annotations. For more details on Seurat usage and data structures, refer to the Seurat tutorials at this link.
The original objects were created using Seurat version 1.4 (October 2016) and have since been updated for compatibility with Seurat version 2.3.4 (`.Robj` files) and Seurat version 5.3.0 (`.h5seurat` files). ANNOTATION FILES Genome annotation RefFlat files with the extended annotations (extension based on MACE results). annChrPicBel_19Apr2016.refFlat (turtle) lizard_annotation.refFlat (lizard) Functional annotation EGGNOG chrysemys_eggnog_pruned.txt (turtle) pogona_eggnog_pruned.txt (lizard) mus_eggnog_pruned.txt (mouse) homo_eggnog_pruned.txt (human) These files were generated from the functional annotations of turtle, lizard, mouse and human genes produced by EggNOG Mapper.
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The original EggNOG Mapper annotations were pruned to remove ambiguous terms (e.g. one-to-many assignments). Matching functional annotations were used to identify one-to-one orthologs across species. Transcription factors list 170712_TFs_list_ensembl.txt List of human transcription factors, annotated in ENSEMBL under the GO terms GO:0003700 (transcription factor activity), GO:0003702 (RNA polymerase II transcription factor activity), GO:0003709 (RNA polymerase III transcription factor activity), GO:0016563 (transcriptional activator activity) and GO:0016564 (transcriptional repressor activity).
Links
Where it is published
- Dataverse dataset page edmond.mpg.de/dataset.xhtml?persistentId=doi%3A10.17617%2F3.OODZLY ↗
landing page · from edmond mpdl mpg de
- DOI doi.org/10.17617/3.oodzly ↗
DOI / persistent id · from edmond mpdl mpg de
Catalogue records · 1
- Dataverse API edmond.mpg.de/api/datasets/:persistentId/?persistentId=doi%3A10.17617%2F3.OO… ↗
metadata API · from edmond mpdl mpg de
Topics
- From keywords
- Astronomy & Astrophysics · Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Humanities · Life Sciences · Life Sciences · Materials Science · Medicine & Health · Ocean & Atmospheric Science · Physics · Social Science
- Inferred from text
- RNA sequencing 65% · Single-cell RNA sequencing 65% · Zoology 74%
Provenance · 2 source records, 25 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Edmond | doi:10.17617/3.OODZLY | 10 d ago | JSON v1 |
| Edmond | doi:10.17617/3.OODZLY | 9 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3109 | enrichment · edmond mpdl mpg de | taxonomy-embedding@1.0.0 | title+keywords+description (74%) |
| concepts[field].dataverse_subject:biology | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /subjects |
| concepts[field].dataverse_subject:biology | source · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:astronomy | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:materials-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:physics | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[modality].local:modality:rna-seq | enrichment · edmond mpdl mpg de | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · edmond mpdl mpg de | keyword-concept-rules@1.0.0 | title+description (65%) |
| created_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| description | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /description |
| publication_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| title | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /name |
| updated_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| version_label | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 |