cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3635822_d7
title: Additional file 10: of Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca

description: ANOVA one-way comparing the expression levels of selected transcripts obtained by RT-qPCR among the four groups (LC_H, LC_X, OG_H, OG_X). Post hoc multiple comparisons using the Tukey HSD test of individual averages of expression levels. A p-value lower than 0.05 (in bold) indicates that expression levels of single transcripts are significantly different. Significance level was set at 5 % (α = 0.05) for F- and p-values. Df indicates the degree of freedom between groups. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3635822_d8
title: Additional file 6: of Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca

description: Differentially expressed transcripts in comparison of cv Leccino vs Ogliarola salentina infected by Xylella fastidiosa. Each unique transcript is categorized by MapMan and Log2Fold expression values calculated by DESeq2 analysis. Transcript categorization was further verified by BLASTX search against nr database. Up- and down-regulated transcripts of both cultivars are in separate excel sheets. (XLSX 10197Â kb)
DOI: 10.6084/m9.figshare.c.3635822_d10
title: Additional file 4: of Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca

description: Differentially expressed transcripts in cv Ogliarola salentina infected by Xylella fastidiosa. Each unique transcript is categorized by MapMan and Log2 fold expression values calculated by DESeq2 analysis. Transcript categorization was further verified by BLASTX search against nr database. Up- and down-regulated transcripts are in separate excel sheets. (XLSX 10155Â kb)
DOI: 10.6084/m9.figshare.c.3635846_d1
title: Additional file 1: Figure S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

description: Phylogenetic tree of M complete sequences from this study. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.c.3635846_d2
title: Additional file 2: Table S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

description: Haplogroup M in Saudi Arabia. In bold haplotypes from this study. Table S2. Super-haplogroup Ages and Geographic links. Table S3. Haplogroup M geographic ranges and ages in kiloyears (kya). Table S4. Populations used in the AMOVA and k-means clustering analyses. Table S5. Mitochondrial DNA M haplogroup ages and coordinates for their respective geographic centers used in the correlation analysis. Table S6. Modern human oldest fossil dating in different regions of Asia and oldest archaeological dating at the eastern side of the Wallace Line. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.c.3635849_d1
title: Additional file 5: of The phylogeny of brown lacewings (Neuroptera: Hemerobiidae) reveals multiple reductions in wing venation

description: Nexus file with instructions for Mr. Bayes. (ZIP 18.1 kb)
DOI: 10.6084/m9.figshare.c.3635903_d2
title: Additional file 2: Table S2. of Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

description: Containing the dRNA-Seq results. Summary of all of the TSSs identified by the dRNA-Seq approach and the additional selected parameters, e.g., replicon, localization, strand, identification in the three datasets, TSS class, associated gene, and promoter score. The first Excel sheet contains the results, and the second Excel sheet contains a list of columns and definitions. (XLSX 572 kb)
DOI: 10.6084/m9.figshare.c.3635903_d1
title: Additional file 1: Table S1. of Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

description: Summarizing the statistics of sequencing and read mapping. For each of the six sequencing runs (three with, three without TEX treatment) the number of reads, the number of mapped reads, etc. are tabulated. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3635906_d1
title: Additional file 4: Table S3. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: Literature-curated dataset of flu-targeting Abs. (CSV 25 kb)
DOI: 10.6084/m9.figshare.c.3635906_d2
title: Additional file 6: Table S5. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: TIV-responding genes for each patient, B cell data. (CSV 3 kb)
DOI: 10.6084/m9.figshare.c.3635906_d4
title: Additional file 9: Table S7. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: Results for individual gene test for convergence, B cell data. (CSV 5 kb)
DOI: 10.6084/m9.figshare.c.3635906_d6
title: Additional file 5: Table S4. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: P values for FPCA-based test. (CSV 19 kb)
DOI: 10.6084/m9.figshare.c.3635906_d8
title: Additional file 10: Table S8. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: Results for individual gene test for convergence, PBMC data. (CSV 4 kb)
DOI: 10.6084/m9.figshare.c.3635906_d7
title: Additional file 7: Table S6. of Statistical inference of a convergent antibody repertoire response to influenza vaccine

description: TIV-responding genes for each patient, PBMC data. (CSV 3 kb)
DOI: 10.6084/m9.figshare.c.3635972_d1
title: MOESM1 of MYC copy gain, chromosomal instability and PI3K activation as potential markers of unfavourable outcome in trastuzumab-treated patients with metastatic breast cancer

description: Additional file 1. Supplemental tables S1 to S10.
DOI: 10.6084/m9.figshare.c.3636005_d1
title: Additional file 1: Table S1. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: Clinical features of AD and control samples. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3636005_d2
title: Additional file 11: Table S7. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: SNPs within DMRs exhibiting strong LD with AD GWAS hits and brain eQTLs. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3636005_d4
title: Additional file 2: Table S2. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: Technical replication of six 450Â K CpGs using the targeted Sequenom EpiTYPER assays. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.c.3636005_d5
title: Additional file 6: Table S3. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: CpGs in significant DMRs with annotation. (XLSX 689 kb)
DOI: 10.6084/m9.figshare.c.3636041_d4
title: Additional file 3: of A robust prognostic gene expression signature for early stage lung adenocarcinoma

description: TCGA LUSC clinical data. (TXT 124 kb)
DOI: 10.6084/m9.figshare.c.3636047_d2
title: Additional file 17: Table S3. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Transcription rate analysis. Transcription rates were fitted for genes in individual polycistronic transcription units that share a common transcription initiation region. The lists of genes used are in the following sheets. The top sheet also shows calculations for some other transcription units. (XLSX 43Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d1
title: Additional file 6: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-F (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d3
title: Additional file 14: Table S2. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Sheet 1: Results for coding regions present in both sheets 1 and 2 of Additional file 9: Table S1 are compared, using PC-A and BS-D for modelling. Column “BS ratio/PC ratio” is column M divided by column H and indicates possible developmental regulation of processing. Column O: “1. BS low”: mRNA amount is at least 4 times less than expected in bloodstream forms; “2. PC Low”: mRNA amount is at least 4 times less than expected in procyclic forms; 3. Both low: mRNA amount is at least 4 times less than expected in both forms; 4. Normal: remaining genes, except for “5. BS high”: mRNA amount is at least 4 times more than expected in bloodstream forms. Data for 5′-UTRs and upstream ORFs are from TritrypDB. Sheet 2: mRNAs that were at least 4 times less abundant than predicted in bloodstream forms, and more abundant than predicted procyclic forms. Sheet 3: mRNAs that were at least 4 times less abundant than predicted in both bloodstream and procyclic forms. Note that columns Q and R are not independent since each includes the mRNA abundance. Sheet 4: Statistical analyses. Sequence information was taken from from TritrypDB. (XLSX 796 kb)
DOI: 10.15468/dl.9faq47
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-140.93609 68.68635,-139.83559 60.60005,-133.80675 60.07372,-130.79233 58.7579,-123.90223 62.44219,-140.93609 68.68635))",
 "OccurrenceStatus is Present",
 "TaxonKey is Limnephilus hageni Banks, 1930"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033850-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3636047_d6
title: Additional file 2: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-B (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d8
title: Additional file 4: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-D (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d7
title: Additional file 7: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model PC-A (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d9
title: Additional file 5: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-E (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d11
title: Additional file 18: Table S4. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Ribosome profiling data. Jensen - data from [20]; Silicotryp - data from [16] and this paper. All numbers were suitably rounded after the calculations had been finished. Gene annotation is partly from tritrypDB and partly manual. Sheet 1: Raw read counts for all ORFs. RP = ribosome profiling, FR = fragmented poly(A) + RNA. BS = bloodstream, PC = procyclic. Sheet 2: Reads for the unique gene set of genes [9], used in subsequent calculations. Sheet 3: DeSeq comparison of Jensen and Silicotryp results (total ribosome profiling reads per ORF) for procyclic forms. Sheet 4: DeSeq comparison of Jensen and Silicotryp results (total ribosome profiling reads per ORF) for bloodstream forms. Sheet 5: DeSeq comparison of Jensen and Silicotryp results (total fragmented RNA reads per ORF) for procyclic forms. Sheet 6: DeSeq comparison of Jensen and Silicotryp results (total fragmented RNA reads per ORF) for bloodstream forms. Sheet 7: ORFs that showed significant differences in ribosome profiling reads between the Jensen and Silicotryp datasets. Red are higher in Silicotryp and blue are lower. Sheet 8: Reads per million calculated for the unique gene set. Sheet 9: Alignment statistics. rp = ribosome profiling; fr = fragmented poly(A) + RNA. PC- = procyclic, BS = cultured bloodstream forms. Sheet 10: Alternative normalisation using EdgeR. (XLSX 7622 kb)
DOI: 10.6084/m9.figshare.c.3636047_d10
title: Additional file 3: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-C (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d15
title: Additional file 8: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model PC-B (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d16
title: Additional file 13: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for polypyrimidine tract analysis (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d18
title: Additional file 1: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-A (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d19
title: Additional file 9: Table S1. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Datasets used for modelling, with results. Data are taken from [16]. Sheet 1: We chose coding regions for which there had been no more than 2-fold differences in either copy number, or mRNA abundances, between 2 different experiments in bloodstream forms. The error in the half-life measurement in bloodstream forms (residual sum of squares) was also less than 0.3. Sim = simulated results; results for model BS-D (columns L & M) were used for the main analyses but those for BS-A and BS-E are also included in columns R-U. Column P has the following categories: “1. High”: mRNA amount is at least 4 times higher than expected; “2. Low”: mRNA amount is at least 4 times less than expected; 3. Normal: mRNA amount is less than 4 times more or less than expected. Column Q is like column P except that the boundary is within 2-fold. Sheet 2: As for sheet 1, but for procyclic forms. In this case mRNAs were taken for which the standard deviation of 3 abundance measurements was less than twice the mean. Sim = simulated results; results for model parameters PC-A (columns L & M) were used for the main analyses but those for PC-B are also included in columns R&S. Sheet 3: Coding regions from sheet 1 for which there was a measured bloodstream-form splicing time of less than 5 min; used for testing all bloodstream-form models except BS-C. Sheet 4: Coding regions from Sheet 4 for which the next gene downstream also had a measured splicing time of less than 5 min; used for testing bloodstream-form model BS-C. (XLSX 1679 kb)
DOI: 10.15468/dl.chmq76
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "Geometry POLYGON ((-97.03333 18.53333, -96.83333 18.53333, -96.83333 18.78333, -97.03333 18.78333, -97.03333 18.53333))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 118 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033851-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10792251
title: Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response

description: Summary

The DNA-damaging agent gemcitabine (GEM) is a first-line treatment for pancreatic cancer but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs including kinase inhibitors but the experimental evidence for such rational is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 146 clinical targeted inhibitors and observed strong synergy for the ATR inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway including phosphorylated pS468 of CHEK1 as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.

Dataset description

This repository contains processed data from S. Höfer et al. 2024. All curve data provided in Kinobeads.zip and decryptM.zip was processed with CurveCurator v0.4.1 (github.com/kusterlab/curve_curator). The code for data processing prior to CurveCurator can be found on Github (github.com/kusterlab/Gem_synergy), and Github_input.zip contains the required input files.
DOI: 10.5281/zenodo.10792252
title: Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response

description: Summary

The DNA-damaging agent gemcitabine (GEM) is a first-line treatment for pancreatic cancer but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs including kinase inhibitors but the experimental evidence for such rational is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 146 clinical targeted inhibitors and observed strong synergy for the ATR inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway including phosphorylated pS468 of CHEK1 as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.

Dataset description

This repository contains processed data from S. Höfer et al. 2024. All curve data provided in Kinobeads.zip and decryptM.zip was processed with CurveCurator v0.4.1 (github.com/kusterlab/curve_curator). The code for data processing prior to CurveCurator can be found on Github (github.com/kusterlab/Gem_synergy), and Github_input.zip contains the required input files.
DOI: 10.6084/m9.figshare.c.3636080_d6
title: Additional file 3: of Nilotinib (Tasignaâ ˘) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial

description: List of 651 intrinsic genes used to cluster nilotinib samples in Fig.Â  2 . Gene symbols are color-coded based on their association with inflammatory (purple), normal-like (green) or fibroproliferative (red) intrinsic subsets. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3636086_d4
title: Additional file 2: of 
                     Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis

description: Protein identification after proteomics analysis. (XLS 461 kb)
DOI: 10.6084/m9.figshare.c.3636089_d2
title: Additional file 3: Table S1, S2 and S3. of Proton irradiation induces persistent and tissue-specific DNA methylation changes in the left ventricle and hippocampus

description: Significant DMRs and DHMRs annotated with the closest RefSeq transcriptional start site. (XLS 9469 kb)
DOI: 10.6084/m9.figshare.c.3636092_d2
title: Additional file 1: of Sex differences in DNA methylation assessed by 450Â K BeadChip in newborns

description: Sex-associated autosomal DMPs. Results for all significant autosomal DMPs associated with sex in CHAMACOS newborns ranked by P value. (CSV 150Â kb)
DOI: 10.6084/m9.figshare.c.3636092_d3
title: Additional file 4: of Sex differences in DNA methylation assessed by 450Â K BeadChip in newborns

description: Sex-associated DMRs. Results for all significant DMRs associated with sex in CHAMACOS newborns ranked by P value. (CSV 449Â kb)
DOI: 10.6084/m9.figshare.c.3636092_d4
title: Additional file 3: of Sex differences in DNA methylation assessed by 450 K BeadChip in newborns

description: Summary of sex-associated DMRs. Number of DMRs significantly hyper- and hypo-methylated in newborn girls compared to boys at FDR multiple testing threshold (q
DOI: 10.6084/m9.figshare.c.3636140_d3
title: Additional file 2 of Assisted transcriptome reconstruction and splicing orthology

description: Results.tar. Compressed folder containing csv files listing the results. (GZ 3942 kb)
DOI: 10.6084/m9.figshare.c.3636230_d1
title: MOESM1 of Semiautomatic segmentation of the kidney in magnetic resonance images using unimodal thresholding

description: Additional file 1. unimodcode.zip: a zipped folder containing the following files: unimodscript.py: the central script for the unimodal thresholding approach, l03threshSTD.py: the monomodal thresholding algorithm function, l02shrink.py: a function to remove most of the whitespace from a masked volume, detect_peaks.py: the peak detection function by Marcos Duarte, also available at https://github.com/demotu/BMC/blob/master/functions/detect_peaks.py , example.nii.gz: an anonymized abdominal MRI in NIfTI format, example_left_kidney_preseg.nii.gz: a manual pre-segmentation of the left kidney of the example MRI, done with the Multi-image Analysis GUI (MANGO), available at http://ric.uthscsa.edu/mango/ , example_right_kidney_preseg.nii.gz: a manual pre-segmentation of the right kidney of the example MRI, done with the Multi-image Analysis GUI (MANGO), available at http://ric.uthscsa.edu/mango/ , LICENSE.txt: the MIT license text, readme.txt: description of the included files, list of dependencies, instructions for installation and use.
DOI: 10.15468/dl.68yrg5
title: Occurrence Download

description: A dataset containing 6926 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "Geometry POLYGON ((-93.21167 15.15278, -92.56778 15.15278, -92.56778 15.95056, -93.21167 15.95056, -93.21167 15.15278))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 6926 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033852-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.