Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

<p>Single-cell RNA-seq datasets from turtle and lizard samples, provided as Seurat objects in both .Robj and .h5seurat formats. 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 <a href="http://satijalab.org/seurat/">this link</a>.</p>
<p>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 (<i>`.Robj`</i> files) and Seurat version 5.3.0 (<i>`.h5seurat`</i> files).</p>
<h3>ANNOTATION FILES</h3>
<b>Genome annotation</b>
<p>RefFlat files with the extended annotations (extension based on MACE results). </p>
<ul>
<li>annChrPicBel_19Apr2016.refFlat (turtle)</li>
<li>lizard_annotation.refFlat (lizard)</li>
</ul>
<b>Functional annotation EGGNOG</b>
<ul>
<li>chrysemys_eggnog_pruned.txt (turtle)</li>
<li>pogona_eggnog_pruned.txt (lizard)</li>
<li>mus_eggnog_pruned.txt (mouse)</li>
<li>homo_eggnog_pruned.txt (human)</li>
</ul>
<p>These files were generated from the functional annotations of turtle, lizard, mouse and human genes produced by <a href="http://eggnogdb.embl.de/">EggNOG Mapper</a>. 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.</p>
<b>Transcription factors list</b>
<i>170712_TFs_list_ensembl.txt</i>
<p>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).</p>