| _version_ | 1866901751295115264 |
|---|---|
| author | Joshi, Piyush |
| author_facet | Joshi, Piyush |
| contents | <p>Raw and processed data associated with single-cell multi-omics human hindbrain atlas described in the manuscript, titled: "A multi-omics altas of human hindbrain development".</p> <p><br><strong>Raw data:</strong></p> <ol> <li>snRNAseq.tar.gz :Unfiltered gene matrices for the 107 snRNA-seq libraries. Both intronic (GeneFull) and exonic (Gene) counts are provided.</li> <li>snATACseq.tar.gz: Raw and filtered peak counts matrices for the 84 snATAC-seq libraries. . </li> <li>combinedcountsHB.RData: Combined gene-counts matrix for the hindbrain atlas. The SingleCellExperiment object name is com.sce. The gene-counts are post-processing, inlcuding removing cell debris, background and doublets.</li> <li>combinedcountsPA.RData, combinedcountsDMG.RData and combinedcountsPfA.RData: Combined gene-counts matrix for the pediatric glial tumor data for PA, DMG and PFA cohort. The SingleCellExperiment object name is com.sce. The gene-counts are post-processing, inlcuding removing cell debris, background and doublets.</li> </ol> <p> </p> <p><strong>Extended data:</strong></p> <ol> <li>Ext. Data 1. Gene ontology terms per meta-gene program. A .txt file listing GO:BP and REAC terms identified per meta-gene program. Only the top ranked (by adj. p-value) term is shown, and all ancestors and descendants of that term is removed.</li> <li>Ext. Data 2. Marker gene-set per class in the transcriptomic atlas.A .RData file with two objects. GSEA_w and GSEA_t are list of marker genes obtained from 'wilcox' and 't' option in scran::findMarkers().</li> <li>Ext. Data 3. Marker CREs per class and cluster. A .bed file. Columns specifify which region is a marker for cluster(s) (top 500 or less) or class (10000 max or less).</li> <li>Ext. Data 4. Cis-regulatory islands per class. A .txt file specifiying CRI regions (max 150, ranked by intensity) identified per class and number of constituting CREs.</li> <li>Ext. Data 5. Bed files per meta-cis-regulatory program. 57 .bed files listing CRE regions (500 bp length) per meta-regulatory program.</li> <li>Ext. Data 6. MEME-format identified seqlets. A .motif file specifiying 165 seqlets identfied from TFMoDIsco based analysis of patterns identified in the 57 meta-regulatory programs.</li> <li>Ext. Data 7. TOMTOM based annotation of seqlets to best matching TF motifs.A .html file showng comparison of seqlets/motifs obtaned in Ext. Data 6 to known JASPAR 2024 non-redundant vertebrate set using TOM-TOM.</li> <li>Ext. Data 8. TF-GRNs identified per class. A.RData filw with two objects, all_tfs listing the 1796 TF-GRNs identified in 16 classes, and all_grns listing targets per TF-GRN.</li> <li>Ext. Data 9. Gene ontology terms for differentially expressed genes in tumor and tumor microenvironment compartments of PA, DMG and PFA. Three .txt files listing filtered (as in Ext. Data 1) GO:BP and REAC terms per tumor compartment, OPC (oligo), Astro and Microglia, both for up- and down-regulated terms when compared to equivalent cellular compartment in the normal hindbrain.</li> <li>Ext. Data 10. JASPAR 2024 motifs clustered into 159 families. A .meme file listing 159 motif families obtained from clustering JASPAR 2024 non-redundant vertebrate motifs used for initialization for DeepHB model.</li> <li>Ext. Data 11. TF-GRNs identified in lower rhombic lip lineage. A .RData file with object(GSEA) listing TF-GRNs identified in pontine nuclei lineage.</li> </ol> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18214927 |
| institution | Zenodo |
| language | |
| publishDate | 2027 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | A multi-omics atlas of human hindbrain development. Joshi, Piyush snRNAseq snATACseq <p>Raw and processed data associated with single-cell multi-omics human hindbrain atlas described in the manuscript, titled: "A multi-omics altas of human hindbrain development".</p> <p><br><strong>Raw data:</strong></p> <ol> <li>snRNAseq.tar.gz :Unfiltered gene matrices for the 107 snRNA-seq libraries. Both intronic (GeneFull) and exonic (Gene) counts are provided.</li> <li>snATACseq.tar.gz: Raw and filtered peak counts matrices for the 84 snATAC-seq libraries. . </li> <li>combinedcountsHB.RData: Combined gene-counts matrix for the hindbrain atlas. The SingleCellExperiment object name is com.sce. The gene-counts are post-processing, inlcuding removing cell debris, background and doublets.</li> <li>combinedcountsPA.RData, combinedcountsDMG.RData and combinedcountsPfA.RData: Combined gene-counts matrix for the pediatric glial tumor data for PA, DMG and PFA cohort. The SingleCellExperiment object name is com.sce. The gene-counts are post-processing, inlcuding removing cell debris, background and doublets.</li> </ol> <p> </p> <p><strong>Extended data:</strong></p> <ol> <li>Ext. Data 1. Gene ontology terms per meta-gene program. A .txt file listing GO:BP and REAC terms identified per meta-gene program. Only the top ranked (by adj. p-value) term is shown, and all ancestors and descendants of that term is removed.</li> <li>Ext. Data 2. Marker gene-set per class in the transcriptomic atlas.A .RData file with two objects. GSEA_w and GSEA_t are list of marker genes obtained from 'wilcox' and 't' option in scran::findMarkers().</li> <li>Ext. Data 3. Marker CREs per class and cluster. A .bed file. Columns specifify which region is a marker for cluster(s) (top 500 or less) or class (10000 max or less).</li> <li>Ext. Data 4. Cis-regulatory islands per class. A .txt file specifiying CRI regions (max 150, ranked by intensity) identified per class and number of constituting CREs.</li> <li>Ext. Data 5. Bed files per meta-cis-regulatory program. 57 .bed files listing CRE regions (500 bp length) per meta-regulatory program.</li> <li>Ext. Data 6. MEME-format identified seqlets. A .motif file specifiying 165 seqlets identfied from TFMoDIsco based analysis of patterns identified in the 57 meta-regulatory programs.</li> <li>Ext. Data 7. TOMTOM based annotation of seqlets to best matching TF motifs.A .html file showng comparison of seqlets/motifs obtaned in Ext. Data 6 to known JASPAR 2024 non-redundant vertebrate set using TOM-TOM.</li> <li>Ext. Data 8. TF-GRNs identified per class. A.RData filw with two objects, all_tfs listing the 1796 TF-GRNs identified in 16 classes, and all_grns listing targets per TF-GRN.</li> <li>Ext. Data 9. Gene ontology terms for differentially expressed genes in tumor and tumor microenvironment compartments of PA, DMG and PFA. Three .txt files listing filtered (as in Ext. Data 1) GO:BP and REAC terms per tumor compartment, OPC (oligo), Astro and Microglia, both for up- and down-regulated terms when compared to equivalent cellular compartment in the normal hindbrain.</li> <li>Ext. Data 10. JASPAR 2024 motifs clustered into 159 families. A .meme file listing 159 motif families obtained from clustering JASPAR 2024 non-redundant vertebrate motifs used for initialization for DeepHB model.</li> <li>Ext. Data 11. TF-GRNs identified in lower rhombic lip lineage. A .RData file with object(GSEA) listing TF-GRNs identified in pontine nuclei lineage.</li> </ol> |
| title | A multi-omics atlas of human hindbrain development. |
| topic | snRNAseq snATACseq |
| url | https://doi.org/10.5281/zenodo.18214927 |