cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.12401030.v1
title: Supplemental Table 1: Sample summary -- Chicken embryonic gonads exposed to ethynylestradiol or vehicle: Genetic Sex, Feminization Sore, CYP19A1 expression and rank, and RNAseq mapped read number

description: Supplemental Table 1 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 1: Sample summary<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table summarizes sample ID, genetic sex, feminization sore, CYP19A1 expression and rank, and RNAseq mapped read number<br>
DOI: 10.35092/yhjc.12401141
title: Supplemental Table 2: RNAseq data of chicken embryonic gonads exposed to ethynylestradiol or vehicle: Expression of protein-coding genes

description: Supplemental Table 2 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 2: RNAseq normalized CPM.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows TMM-normalized RNA-seq data (counts per million) of these chicken embryonic gonads for expression of protein-coding genes annotated in the chicken reference genome sequence galGal3.<br>
DOI: 10.35092/yhjc.12401141.v1
title: Supplemental Table 2: RNAseq data of chicken embryonic gonads exposed to ethynylestradiol or vehicle: Expression of protein-coding genes

description: Supplemental Table 2 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 2: RNAseq normalized CPM.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows TMM-normalized RNA-seq data (counts per million) of these chicken embryonic gonads for expression of protein-coding genes annotated in the chicken reference genome sequence galGal3.<br>
DOI: 10.35092/yhjc.12401147
title: Supplemental Table 3: List of genes induced or suppressed in chicken embryonic gonads by in ovo exposure to ethynylestradiol

description: Supplemental Table 3 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 3: Cluster Genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows genes induced or suppressed by exposure to ethynylestradiol determined by RNA-seq.
DOI: 10.35092/yhjc.12401147.v1
title: Supplemental Table 3: List of genes induced or suppressed in chicken embryonic gonads by in ovo exposure to ethynylestradiol

description: Supplemental Table 3 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 3: Cluster Genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows genes induced or suppressed by exposure to ethynylestradiol determined by RNA-seq.
DOI: 10.35092/yhjc.12401153
title: Supplemental Table 4: List of genes differentially expressed in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 4 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 4: Differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.<br>Each tag shows a list of DEGs with gene symbols, log2 fold changes (logFC), average log2 counts-per-million expression (logCPM), likelihood ratio statistics (LR) (1), p-values, and false discovery ratio (FDR) (2) calculated based on the generalized linear model (3). DEGs listed in each spreadsheet are selected using criteria indicated in the tags. For example, “FS0 vs FS1” indicates genes differentially expressed between FS=0 and FS=1 gonads. The spreadsheet “FS0 &lt; FS1 or FS2” lists genes whose expression in weaker in FS=0 compared to either FS=1 or FS=2. The spreadsheet “FS0 vs FS1 not FS3 UP” lists genes upregulated in FS=1 compared to FS=0, but genes upregulated in FS=3 compared to FS=0 were removed from this list.<br>[References]1. Xu M, Chen L. An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq. Brief Bioinform. 2018;19(1):109-117.2. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003;19(3):368-375.3. Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol. 2014;1150:45-79.
DOI: 10.35092/yhjc.12401153.v1
title: Supplemental Table 4: List of genes differentially expressed in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 4 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 4: Differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.
DOI: 10.35092/yhjc.12401156
title: Supplemental Table 5: List of genes following various profiles of feminization-dependent expression in chicken embryonic gonads after in ovo exposure to ethynylestradiol

description: Supplemental Table 5 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 5: Classified differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads following various profiles of feminization-dependent expression after in ovo exposure to ethynylestradiol determined by RNA-seq. Names of the representative feminization-dependent profiles are shown in the tag labels.
DOI: 10.35092/yhjc.12401156.v1
title: Supplemental Table 5: List of genes following various profiles of feminization-dependent expression in chicken embryonic gonads after in ovo exposure to ethynylestradiol

description: Supplemental Table 5 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 5: Classified differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads following various profiles of feminization-dependent expression after in ovo exposure to ethynylestradiol determined by RNA-seq. Names of the representative feminization-dependent profiles are shown in the tag labels.
DOI: 10.35092/yhjc.12401162
title: Supplemental Table 6: Gene ontology analysis of the CTNNB1 profile feminization-suppressible genes in chicken embryonic gonads after in ovo exposure to ethynylestradiol

description: Supplemental Table 6 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 6: Gene ontology analysis of CTNNB1 group differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. Expression of several genes, represented by CTNNB1, in chicken embryonic gonads were strongly suppressed upon feminization after in ovo exposure to ethynylestradiol. This table shows outcome of a gene ontology analysis of the CTNNB1 group genes using the NIH LHRI DAVID service.
DOI: 10.35092/yhjc.12401165
title: Supplemental Table 7: RNAseq data of chicken embryonic gonads exposed to ethynylestradiol or vehicle: Expression of repetitive sequences

description: Supplemental Table 7 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 7: Normalized repetitive sequence expression.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows TMM-normalized RNA-seq data (counts per million) of these chicken embryonic gonads for expression of repetitive sequences annotated by RepeatMasker in the chicken reference genome sequence galGal6.
DOI: 10.35092/yhjc.12401165.v1
title: Supplemental Table 7: RNAseq data of chicken embryonic gonads exposed to ethynylestradiol or vehicle: Expression of repetitive sequences

description: Supplemental Table 7 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 7: Normalized repetitive sequence expression.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows TMM-normalized RNA-seq data (counts per million) of these chicken embryonic gonads for expression of repetitive sequences annotated by RepeatMasker in the chicken reference genome sequence galGal6.
DOI: 10.35092/yhjc.12401171
title: Supplemental Table 8: List of genes differentially expressed repetitive sequences in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 8 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 8: Differentially expressed repetitive sequences.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed repetitive sequences in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.
DOI: 10.35092/yhjc.12401171.v1
title: Supplemental Table 8: List of genes differentially expressed repetitive sequences in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 8 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 8: Differentially expressed repetitive sequences.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed repetitive sequences in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.
DOI: 10.35092/yhjc.12401177
title: Supplemental Table 9: List of genes showing differential promoter methylation in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 9 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 9: Genes with differentially methylated regions on transcriptional start sites.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of genes showing differemtial promoter methylation in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.<br>This table shows 6 groups of TSS linked to differentially methylated genes (TDMGs) – namely, FS0 &gt; FS3 (demethylated in FS=3 normal ovaries but not in FS=0 normal ZZ-testes; 341 TDMGs), FS0 &lt; FS3 (3243 TDMGs), FS0 &gt; FS1/2 (927 TDMGs), FS0 &lt; FS1/2 (5352 TDMGs), FS3 &gt; FS1/2 (6535 TDMGs), and FS3 &lt; FS1/2 (1696 TDMGs). <br>
DOI: 10.35092/yhjc.12401177.v1
title: Supplemental Table 9: List of genes showing differential promoter methylation in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 9 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 9: Genes with differentially methylated regions on transcriptional start sites.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of genes showing differemtial promoter methylation in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.
DOI: 10.35092/yhjc.12420881
title: OCR results from 65k pathway figures published between 1995 and 2019

description: In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. First, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Then, we performed OCR to extract recognized human gene symbols from the images. Altogether, we identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts.<br>This supplementary file contains the tidy results from optical character recognition (OCR) on 65k pathway figures published between 1995 and 2019. Columns include:<br>1. <b>figid</b> - Unique figure identifier: concatenation of PMCID and figure filename2. <b>pmcid</b> - PubMed Central Identifier3. <b>word</b> - Character string extracted by OCR and eventually matched to human HGNC lexicon4. <b>symbol</b> - Transformed word that matched lexicon5. <b>source</b> - Source of lexicon that matched symbol6. <b>hgnc_symbol</b> - Official human gene symbol7. <b>entrez</b> - Official NCBI Gene identifier<br>
DOI: 10.35092/yhjc.12420881.v1
title: OCR results from 65k pathway figures published between 1995 and 2019

description: In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. First, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Then, we performed OCR to extract recognized human gene symbols from the images. Altogether, we identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts.<br>This supplementary file contains the tidy results from optical character recognition (OCR) on 65k pathway figures published between 1995 and 2019. Columns include:<br>1. <b>figid</b> - Unique figure identifier: concatenation of PMCID and figure filename2. <b>pmcid</b> - PubMed Central Identifier3. <b>word</b> - Character string extracted by OCR and eventually matched to human HGNC lexicon4. <b>symbol</b> - Transformed word that matched lexicon5. <b>source</b> - Source of lexicon that matched symbol6. <b>hgnc_symbol</b> - Official human gene symbol7. <b>entrez</b> - Official NCBI Gene identifier<br>
DOI: 10.35092/yhjc.12420887
title: 65k pathway figures published between 1995 and 2019

description: In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. First, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Then, we performed OCR to extract recognized human gene symbols from the images. Altogether, we identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts.<br>This supplementary file contains the tidy results from identification of 65k pathway figures published between 1995 and 2019. Columns include:<br>1. <b>figid</b> - Unique figure identifier: concatentation of PMCID and figure filename (see 11 and 12)<br>2. <b>number</b> - Figure number in parent paper3. <b>reftext</b> - Citation for parent paper4. <b>year</b> - Publication year of parent paper5. <b>pathway_score</b> - Pathway likelihood score from machine learning6. <b>pmc_ranked_result_index</b> - Ranking from original PubMed Central query result7. <b>figtitle</b> - Figure title in parent paper8. <b>papertitle</b> - Title of parent paper9. <b>caption</b> - Figure caption in parent paper10. <b>figlink</b> - URL to figure<br>11. <b>pmcid</b> - PubMed Central Identifier12. <b>filename</b> - Figure filename<br>13. <b>source_f</b> - Local file path (ignore)14. <b>type.man</b> - Manual classification of pathway (p), composite (c) or other (o)15. <b>automl_index</b> - Stored index from sorting by pathway_score (see 5)<br>
DOI: 10.35092/yhjc.12420887.v1
title: 65k pathway figures published between 1995 and 2019

description: In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. First, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Then, we performed OCR to extract recognized human gene symbols from the images. Altogether, we identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts.<br>This supplementary file contains the tidy results from identification of 65k pathway figures published between 1995 and 2019. Columns include:<br>1. <b>figid</b> - Unique figure identifier: concatentation of PMCID and figure filename (see 11 and 12)<br>2. <b>number</b> - Figure number in parent paper3. <b>reftext</b> - Citation for parent paper4. <b>year</b> - Publication year of parent paper5. <b>pathway_score</b> - Pathway likelihood score from machine learning6. <b>pmc_ranked_result_index</b> - Ranking from original PubMed Central query result7. <b>figtitle</b> - Figure title in parent paper8. <b>papertitle</b> - Title of parent paper9. <b>caption</b> - Figure caption in parent paper10. <b>figlink</b> - URL to figure<br>11. <b>pmcid</b> - PubMed Central Identifier12. <b>filename</b> - Figure filename<br>13. <b>source_f</b> - Local file path (ignore)14. <b>type.man</b> - Manual classification of pathway (p), composite (c) or other (o)15. <b>automl_index</b> - Stored index from sorting by pathway_score (see 5)<br>
DOI: 10.35092/yhjc.12424685
title: MRI dataset supporting "Layer-Specific Contributions to Imagined and Executed Hand Movements in Human Primary Motor Cortex"

description: The data file contains nifti files for each run of each participant in our study. The zipped file also contains a 'readMe' file with more information.<br><br>Dataset supports publication: Persichetti, A. S., Avery, J. A., Huber, L., Merriam, E. P., & Martin, A. (2020). Layer-Specific Contributions to Imagined and Executed Hand Movements in Human Primary Motor Cortex. <i>Current Biology</i>. https://doi.org/10.1016/j.cub.2020.02.046<br>Abstract: The human ability to imagine motor actions without executing them (i.e., motor imagery) is crucial to a number of cognitive functions, including motor planning and learning, and has been shown to improve response times and accuracy of subsequent motor actions [ 1 , 2 ]. Although these behavioral findings suggest the possibility that imagined movements directly influence primary motor cortex (M1), how this might occur remains unknown [ 3 ]. Here, we use a non-blood-oxygen-level-dependent (BOLD) method for collecting fMRI data, called vascular space occupancy (VASO) [ 4 , 5 ], to measure neural activations across cortical laminae in M1 while participants either tapped their thumb and forefinger together or simply imagined doing so. We report that, whereas executed movements (i.e., finger tapping) evoked neural responses in both the superficial layers of M1 that receive cortical input and the deep layers of M1 that send output to the spinal cord to support movement, imagined movements evoked responses in superficial cortical layers only. Furthermore, we found that finger tapping preceded by both imagined and executed movements showed a reduced response in the superficial layers (repetition suppression) coupled with a heightened response in the deep layers (repetition enhancement). Taken together, our results provide evidence for a mechanism whereby imagined movements can directly affect motor performance and might explain how neural repetition effects lead to improvements in behavior (e.g., repetition priming).