--- _id: '7016' abstract: - lang: eng text: Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature. article_processing_charge: No author: - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X citation: ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016 apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016 chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016. ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019. ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016. mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016. short: I. Tomanek, (2019). contributor: - contributor_type: project_leader first_name: Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 date_created: 2019-11-13T09:07:31Z date_published: 2019-11-13T00:00:00Z date_updated: 2024-02-21T12:45:25Z day: '13' ddc: - '576' department: - _id: CaGu doi: 10.15479/AT:ISTA:7016 file: - access_level: open_access checksum: 72441055043eda4cbf1398a422e2c118 content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:52:21Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - amplified. file_id: '7017' file_name: D8_S35_R2_001.fastq file_size: 2456192500 relation: main_file title: Locus1_amplified - access_level: open_access checksum: a4ac50bf655d9c751f0305ade5c2ee16 content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:52:59Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - ancestral. file_id: '7018' file_name: IT028_S11_R2_001.fastq file_size: 2833452234 relation: main_file title: Locus1_ancestral - access_level: open_access checksum: 5b227708ff478ca06e3f0448a4efdc2f content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:54:10Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection. file_id: '7019' file_name: D8-DOG1_S47_R2_001.fastq file_size: 2878017264 relation: main_file title: Locus1_amplified_DOG - access_level: open_access checksum: d9550a4c044116075fa83f8f2ea31d6f content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:54:27Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - amplified. file_id: '7020' file_name: D4_S71_R2_001.fastq file_size: 2180826995 relation: main_file title: Locus2_amplified - access_level: open_access checksum: 466ceb302c020ac013007a879fcde69d content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:55:58Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - ancestral. file_id: '7021' file_name: IT030_S23_R2_001.fastq file_size: 2108826444 relation: main_file title: Locus2_ancestral - access_level: open_access checksum: 8aeb1da771713c7baa5a847eff889604 content_type: application/octet-stream creator: itomanek date_created: 2019-11-21T12:31:01Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection. file_id: '7092' file_name: D4-DOG1_S83_R2_001.fastq file_size: 3144330494 relation: main_file title: Locus2_amplified_DOG - access_level: open_access checksum: bf7d4b053f14af4655fb5574209fdb2d content_type: application/zip creator: itomanek date_created: 2020-01-14T11:22:27Z date_updated: 2020-07-14T12:47:47Z description: Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette. file_id: '7273' file_name: galK_dual_reporter_cassette.gb.zip file_size: 4179 relation: main_file title: DNA sequence of the chromosomal reporter gene cassette - access_level: open_access checksum: 5e91cee2eff6f4a7cde456c6fb07c2ff content_type: text/plain creator: dernst date_created: 2020-01-15T14:15:55Z date_updated: 2020-07-14T12:47:47Z file_id: '7335' file_name: Readme_7016.txt file_size: 435 relation: main_file title: Read_me_sequence_data - access_level: open_access checksum: 5e6745dcfb9c1b11dd935ac3ee45fe33 content_type: application/zip creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z description: FACS data associated with Fig. 2c - see read_me_FACS file_id: '7351' file_name: FACS_data.xlsx.zip file_size: 3765861 relation: main_file title: FACS data - access_level: open_access checksum: a85caf092ae4b17668f70af2d93fad00 content_type: text/rtf creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z file_id: '7352' file_name: read_me_FACS.rtf file_size: 4996 relation: main_file - access_level: open_access checksum: fd8ba5d75d24e47ddf7e70bfdadb40d4 content_type: text/rtf creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z file_id: '7353' file_name: read_me_microfluidics.rtf file_size: 868 relation: main_file - access_level: open_access checksum: 69c5dc5ca5c069a138183c934acc1778 content_type: application/zip creator: itomanek date_created: 2020-01-22T15:44:17Z date_updated: 2020-07-14T12:47:47Z description: microfluidics time trace data - see read_me_microfluidics file_id: '7354' file_name: microfuidics_data.zip file_size: 8141727 relation: main_file title: microfluidics data file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' keyword: - Escherichia coli - gene amplification - galactose - DOG - experimental evolution - Illumina sequence data - FACS data - microfluidics data month: '11' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '7652' relation: used_in_publication status: public status: public title: Data for the paper "Gene amplification as a form of population-level gene expression regulation" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7154' article_processing_charge: No author: - first_name: Ruslan full_name: Guseinov, Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 citation: ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154 apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154 chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154. ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019. ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154. mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154. short: R. Guseinov, (2019). contributor: - first_name: Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 - first_name: Connor last_name: McMahan - first_name: Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - first_name: Chiara last_name: Daraio - first_name: Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 date_created: 2019-12-09T07:52:46Z date_published: 2019-12-06T00:00:00Z date_updated: 2024-02-21T12:45:03Z day: '06' ddc: - '000' department: - _id: BeBi doi: 10.15479/AT:ISTA:7154 ec_funded: 1 file: - access_level: open_access checksum: 155133e6e188e85b3c0676a5e70b9341 content_type: application/x-zip-compressed creator: dernst date_created: 2019-12-09T07:52:17Z date_updated: 2020-07-14T12:47:50Z file_id: '7155' file_name: temporal_morphing_supp_data.zip file_size: 65307107 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publisher: Institute of Science and Technology Austria related_material: record: - id: '8433' relation: used_in_publication status: deleted - id: '7262' relation: used_in_publication status: public status: public title: Supplementary data for "Programming temporal morphing of self-actuated shells" tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6060' article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060 apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060 chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060. ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019. ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060. mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060. short: B. Vicoso, (2019). date_created: 2019-02-28T10:55:15Z date_published: 2019-02-28T00:00:00Z date_updated: 2024-02-21T12:45:42Z day: '28' department: - _id: BeVi doi: 10.15479/AT:ISTA:6060 file: - access_level: open_access checksum: a338a622d728af0e3199cb07e6dd64d3 content_type: application/zip creator: bvicoso date_created: 2019-02-28T10:54:27Z date_updated: 2020-07-14T12:47:17Z file_id: '6061' file_name: SupData.zip file_size: 36646050 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '6418' relation: research_paper status: public status: public title: 'Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). ' type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6074' abstract: - lang: eng text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS." article_processing_charge: No author: - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074 apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074 chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074. ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019. ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074. mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074. short: C. Dotter, G. Novarino, (2019). date_created: 2019-03-07T13:32:35Z date_published: 2019-01-09T00:00:00Z date_updated: 2024-02-21T13:41:01Z day: '09' ddc: - '570' department: - _id: GaNo doi: 10.15479/AT:ISTA:6074 file: - access_level: open_access checksum: bc1b285edca9e98a2c63d153c79bb75b content_type: application/zip creator: dernst date_created: 2019-03-07T13:37:19Z date_updated: 2020-07-14T12:47:18Z file_id: '6084' file_name: Setd5_paper.zip file_size: 33202743 relation: supplementary_material file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' month: '01' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '3' relation: research_paper status: public status: public title: Supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6062' abstract: - lang: eng text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7). article_processing_charge: No author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 citation: ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062 apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062 chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062. ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062. mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062. short: M. Nardin, (2019). date_created: 2019-03-04T14:20:58Z date_published: 2019-03-29T00:00:00Z date_updated: 2024-02-21T12:46:04Z day: '29' department: - _id: JoCs doi: 10.15479/AT:ISTA:6062 file: - access_level: open_access checksum: 48e7b9a02939b763417733239522a236 content_type: application/zip creator: mnardin date_created: 2019-03-05T09:29:37Z date_updated: 2020-07-14T12:47:18Z file_id: '6068' file_name: Online_data.zip file_size: 37002186 relation: main_file title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals" file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '6194' relation: research_paper status: public status: public title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals" tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ...