Single-cell datasets for temporal gene expression integration

<p>Contains loom files and preprocessed adata objects to compare methods for temporal gene expression integration. Loom files can be accessed using the &#39;read&#39; function in Scvelo. Preprocessed adata objects can be accessed using the &#39;read_h5ad&#39; function in Scanpy.</p> <p>The raw single-cell RNA sequencing datasets can be found under the following accession codes.</p> <ul> <li> <p>Mouse embryonic cell cycle dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/nbt.3102">10.1038/nbt.3102</a>) was originally downloaded from ArrayExpress with the accession code E-MTAB-2805</p> </li> <li> <p>Hematopoiesis differentiation dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/10.1182/blood-2016-05-716480</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE81682</p> </li> <li> <p>NKT cell differentiation dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/ni.3437">10.1038/ni.3437</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE74596.</p> </li> <li> <p>Hematopoiesis differentiation dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org</a>/<a href="https://doi.org/10.1038/nature19348">10.1038/nature19348</a>) was originally downloaded from the Gene Expression Omnibus with the accession codes GSE70236, GSE70240, GSE70244</p> </li> <li> <p>LPS stimulation dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1016/j.cels.2017.03.010">10.1016/j.cels.2017.03.010</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE94383.</p> </li> <li> <p>INF-gamma&nbsp;stimulation dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/s41587-020-00803-5">10.1038/s41587-020-00803-5</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE161465.</p> </li> <li> <p>AML chemotherapy dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/s41591-018-0233-1">10.1038/s41591-018-0233-1</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE116481.</p> </li> <li> <p>AML diagnosis/relapse dataset from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/s41375-021-01338-7">10.1038/s41375-021-01338-7</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE126068.</p> </li> <li> <p>MS case control PBMC and CSF datasets from Ref. (<a href="https://doi.org/10.1182/blood-2016-05-716480">https://doi.org/</a><a href="https://doi.org/10.1038/s41467-019-14118-w">10.1038/s41467-019-14118-w</a>) was originally downloaded from the Gene Expression Omnibus with the accession code GSE138266.</p> </li> </ul>