| List of tables on | |||||||||
| Table ID | Reference/ Journal | Folder/File name (data table)/ Table title | Display | Download | Sample/ Stage | Experiment/ Method | Gene | Keys | |
|---|---|---|---|---|---|---|---|---|---|
| T0001 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/TableS1_Hh_signaling_genes_hyperlinkadded.xlsx Table S1. Parasteatoda tepidariorum counterparts of Hedgehog signaling genes |
Display | Download | Hh signaling pathway components na |
homolog search Blast |
hedgehog|hh/patched|ptc/smoothened|smo | ||
| T0002 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/TableS2_hhptc_st5selected_hyperlinkadded.xlsx Table S2. Ninety-eight genes identified in Pt-hh and Pt-ptc pRNAi and RNA-seq experiments at late stage 5 and differentially expressed gene analysis |
Display | Download | hh and ptc pRNAi embryos st_5 |
Identification of DEGs pRNAi_RNAseq |
hedgehog|hh/patched|ptc | ||
| T0003 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/TableS3_msx_st6selected_hyperlinkadded.xlsx Table S3. Forty genes selected from DEGs identified in Pt-msx1 pRNAi and RNA-seq experiments at stage 6 |
Display | Download | msx1|msh pRNAi embryos st_6 |
Identification of DEGs pRNAi_RNAseq |
msx1|msh | ||
| T0004 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/TableS4_primers&clones.xlsx Table S4. Primers and clones |
Display | Download | primers_clones na |
na PCR_EST_RACE |
hedgehog | ||
| T0005 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS1_RNAseq.xlsx Data file S1. Summary of RNA-seq Mapping and HTseq-count |
Display | Download | gfp hh ptc and msx1 pRNAi embryos st_3_5_6 |
sequence reads pRNAi_RNAseq |
gfp/hedgehog|hh/patched|ptc/msx1|msh | ||
| T0006 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS2_count.xlsx Data file S2. Result of HTseq-count per gene |
Display | Download | gfp hh ptc and msx1 pRNAi embryos st_3_5_6 |
mapping read counts pRNAi_RNAseq |
gfp/hedgehog|hh/patched|ptc/msx1|msh | ||
| T0007 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS3_deg_Hh_hyperlinkadded.xlsx Data file S3.1. Differentially expressed genes identified in Pt-hh pRNAi and RNA-seq at early stage 3 |
Display | Download | hh pRNAi embryos st_3 |
Identification of DEGs pRNAi_RNAseq |
hedgehog|hh | ||
| T0008 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS3_deg_Hh_hyperlinkadded.xlsx Data file S3.2. Differentially expressed genes identified in Pt-hh pRNAi and RNA-seq at late stage 5 |
Display | Download | hh pRNAi embryos st_5 |
Identification of DEGs pRNAi_RNAseq |
hedgehog|hh | ||
| T0009 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS4_deg_Ptc_hyperlinkadded.xlsx Data file S4.1. Differentially expressed genes identified in Pt-ptc pRNAi and RNA-seq at early stage 3 |
Display | Download | ptc pRNAi embryos st_3 |
Identification of DEGs pRNAi_RNAseq |
patched|ptc | ||
| T0010 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS4_deg_Ptc_hyperlinkadded.xlsx Data file S4.2. Differentially expressed genes identified in Pt-ptc pRNAi and RNA-seq at late stage 5 |
Display | Download | ptc pRNAi embryos st_5 |
Identification of DEGs pRNAi_RNAseq |
patched|ptc | ||
| T0011 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS6_deg_Msx_hyperlinkadded.xlsx Data file S6.1. Differentially expressed genes identified in Pt-msx1 pRNAi and RNA-seq at late stage 5 |
Display | Download | msx1_msh pRNAi embryos st_3 |
Identification of DEGs pRNAi_RNAseq |
msx1|msh | ||
| T0012 | Akiyama-Oda and Oda (2020) Sci Adv |
2020SciAdv/Data_fileS6_deg_Msx_hyperlinkadded.xlsx Data file S6.2. Differentially expressed genes identified in Pt-msx1 pRNAi and RNA-seq at stage 6 |
Display | Download | msx1_msh pRNAi embryos st_5 |
Identification of DEGs pRNAi_RNAseq |
msx1|msh | ||
| T0013 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS1_Statistics_of_the_first_single-cell_RNA-seq.xlsx Table S1. Statistics of the first single-cell RNA-seq experiment |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq |
|||
| T0014 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS2_445_DEGs_btw_two_ectodermal_clusters_hyperlink.xlsx Table S2. 445 DEGs between two presumptive ectodermal clusters |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq |
|||
| T0015 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS3_Cell_cycle_genes_hyperlink.xlsx Table S3. Cell cycle genes |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq |
cell cycle genes | ||
| T0016 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.0. Cluster 0 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster0 | ||
| T0017 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.1. Cluster 1 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster1 | ||
| T0018 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.2. Cluster 2 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster2 | ||
| T0019 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.3. Cluster 3 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster3 | ||
| T0020 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.4. Cluster 4 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster4 | ||
| T0021 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS4_Cluster_markers_first_single-cell_RNA-seq_hyperlink.xlsx Table S4.5. Cluster 5 markers identified in the first single-cell RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_clustering |
cluster5 | ||
| T0022 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS5_Genes_expressed_specifically_in_CM_cells_hyperlink.xlsx Table S5. Genes expressed specifically in the CM cells |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_template-matching |
CM cell specific genes | ||
| T0023 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS6_Genes_with_similar_pattern_to_cumulus_UMAP_hyperlink.xlsx Table S6. Genes with highly similar pattern to LOC107444265 cumulus expression pattern on the UMAP plot |
Display | Download | wild-type embryos st_5 |
single-cell RNA-seq of early embryos scRNAseq_template-matching |
cumulus specific genes | ||
| T0024 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS7_Statistics_of_the_second_single-cell_and_-nucleus_RNA-seq.xlsx Table S7. Statistics of the second single-cell and the single-nucleus RNA-seq experiment |
Display | Download | wild-type embryos st_5 |
single-cell/nuc RNA-seq of early embryos single-cell/nuc-RNAseq |
|||
| T0025 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS8_85_DEGs_btw_two_ectodermal_clusters_hyperlink.xlsx Table S8. 85 DEGs between two presumptive ectodermal clusters |
Display | Download | wild-type embryos st_5 |
single-cell/nuc RNA-seq of early embryos single-cell/nuc-RNAseq |
|||
| T0026 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS9_Cluster_markers_single-nucleus_RNA-seq_hyperlink.xlsx Table S9.1. Cluster 6 markers identified in the single-nucleus RNA-seq analysis |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster6 | ||
| T0027 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS9_Cluster_markers_single-nucleus_RNA-seq_hyperlink.xlsx Table S9.2. Cluster 9 markers identified in the single-nucleus RNA-seq analysis |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster9 | ||
| T0028 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/TableS10_Clones_hyperlink.xlsx Table S10. Clones |
Display | Download | primers_clones na |
na PCR_EST_cloning |
|||
| T0029 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.1 Cluster 0 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster0 | ||
| T0030 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.2 Cluster 1 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster1 | ||
| T0031 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.3 Cluster 2 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster2 | ||
| T0032 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.4 Cluster 3 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster3 | ||
| T0033 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.5 Cluster 4 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster4 | ||
| T0034 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.6 Cluster 5 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster5 | ||
| T0035 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.7 Cluster 6 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster6 | ||
| T0036 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.8 Cluster 7 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster7 | ||
| T0037 | Akiyama-Oda et al. (2022) Front CDB |
2022FrontCDB/RelatedData1_cluster.markers220620Nuc5lA02_1-42-0.5.xlsx RelatedData1.9 Cluster 8 markers identified in single-nucleus RNA-seq analysis of P. tepidariorum embryos at late stage 5 |
Display | Download | wild-type embryos st_5 |
single-nuc RNA-seq of early embryos single-nuc-RNAseq_clustering |
cluster8 | ||
| T0038 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile2_TableS1_List_of_DEGs_isolated_cells_st3_comp1_hyperlink.xlsx Table S1. List of DEGs between c versus i/p cells from stage-3 embryo (comparison I) |
Display | Download | wild-type embryos st_3 |
RNA-seq of isolated cells RNAseq |
|||
| T0039 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile2_TableS2_List_of_DEGs_isolated_cells_st3_comp2_hyperlink.xlsx Table S2. List of DEGs between p versus c/i cells from stage-3 embryo (comparison II) |
Display | Download | wild-type embryos st_3 |
RNA-seq of isolated cells RNAseq |
|||
| T0040 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile2_TableS3_List_of_DEGs_isolated_cells_st3_comp3_hyperlink.xlsx Table S3. List of DEGs between i versus c/p cells from stage-3 embryo (comparison III) |
Display | Download | wild-type embryos st_3 |
RNA-seq of isolated cells RNAseq |
|||
| T0041 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile2_TableS4_List_of_DEGs_isolated_cells_st4_hyperlink.xlsx Table S4. List of DEGs between c versus p cells from stage-4 embryo |
Display | Download | wild-type embryos st_4 |
RNA-seq of isolated cells RNAseq |
|||
| T0042 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile2_TableS5_List_of_DEGs_isolated_cells_st5e_hyperlink.xlsx Table S5. List of DEGs between c versus p cells from early stage-5 embryo |
Display | Download | wild-type embryos st_5 |
RNA-seq of isolated cells RNAseq |
|||
| T0043 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile4_TableS6_pRNAi_screen_hyperlink.xlsx Table S6. Summary of the pilot pRNAi screen of 19 selected genes |
Display | Download | pRNAi embryos na |
pRNAi screen pRNAi |
|||
| T0044 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile7_TableS7_List_of_bioinformatic_resources_hyperlink.xlsx Table S7. List of bioinformatic resources used for phylogenetic characterization of GATA family members |
Display | Download | sequences na |
transcriptomic resources de novo assembly |
|||
| T0045 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile7_TableS8_amino_acid_sequence_alignment_GATA_hyperlink.xlsx Table S8. Amino acid sequence alignment and classification of GATA family members |
Display | Download | sequences na |
phylogenetic analysis sequence alignment |
GATA|GATA-like|fuchi|srp|serpent|pnr|pannier|grn|grain | ||
| T0046 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile9_TableS9_List_of_DEGs_fuchi_pRNAi_st2_hyperlink.xlsx Table S9. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 2 |
Display | Download | fuchi pRNAi embryos st_2 |
Identification of DEGs pRNAi_RNAseq |
fuchi|fuchi nashi | ||
| T0047 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile9_TableS10_List_of_DEGs_fuchi_pRNAi_st3_hyperlink.xlsx Table S10. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 3 |
Display | Download | fuchi pRNAi embryos st_3 |
Identification of DEGs pRNAi_RNAseq |
fuchi|fuchi nashi | ||
| T0048 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile9_TableS11_List_of_DEGs_fuchi_pRNAi_st5e_hyperlink.xlsx Table S11. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at early stage 5 |
Display | Download | fuchi pRNAi embryos st_5 |
Identification of DEGs pRNAi_RNAseq |
fuchi|fuchi nashi | ||
| T0049 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile10_TableS12_ATAC-seq_peaks_fuchi_pRNAi_hyperlink.xlsx Table S12. Data from comparative analysis of read counts in extracted ATAC-seq peaks between fuchi pRNAi and wild-type embryos |
Display | Download | fuchi pRNAi embryos st_3 |
ATAC-seq of early embryos pRNAi_ATAC-seq |
fuchi|fuchi nashi | ||
| T0050 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile10_TableS13_diff_ATAC-seq_peaks_fuchi_pRNAi_hyperlink.xlsx Table S13. List of differential ATAC-seq peaks between fuchi pRNAi and wild-type embryos at stage 3 (FDR < 0.05) |
Display | Download | fuchi pRNAi embryos st_3 |
ATAC-seq of early embryos pRNAi_ATAC-seq |
fuchi|fuchi nashi | ||
| T0051 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile11_TableS14_ATAC-seq_peaks_hh_pRNAi_hyperlink.xlsx Table S14. Data from comparative analysis of read counts in extracted ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos |
Display | Download | hh pRNAi embryos st_3 |
ATAC-seq of early embryos pRNAi_ATAC-seq |
hedgehog|hh | ||
| T0052 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile11_TableS15_diff_ATAC-seq_peaks_hh_pRNAi_hyperlink.xlsx Table S15. List of differential ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 (FDR < 0.05) |
Display | Download | hh pRNAi embryos st_3 |
ATAC-seq of early embryos pRNAi_ATAC-seq |
hedgehog|hh | ||
| T0053 | Iwasaki-Yokozawa et al. (2022) BMC Biol |
2022BMCbiol/Addfile12_Table16_Primers_and_cDNA_clones_hyperlink.xlsx Table S16. Primers and cDNA clones used for RNAi and in situ hybridization |
Display | Download | primers_clones na |
na PCR_EST_cloning |
|||