cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.22139918.v1
title: Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

description: Bacteria replicate the genome on average once per generation, irrespective of growth condition-dependent changes in generation time and cell size. The strategy appears to be to initiate replication in a narrow chromosome-to-size ratio interval for each growth condition. To investigate how <em>Escherichia coli </em>accurately compares its size to the number of chromosomes, we perturbed some of the mechanisms proposed to achieve this precision and monitored how replication initiation was affected with time-lapse single-cell fluorescence microscopy. We found that the regulatory inactivation of DnaA-ATP (RIDA) mechanism, which converts the replication initiation molecule DnaA to its inactive form in proportion to the number of chromosomes, was the most important factor and that other previously described mechanisms have a less critical role. 
<br>
This dataset contains the raw data, analysis and code needed to generate the figures presented in the paper. The raw data consists of microscopy images, growth rate measurements, RT-qPCR, whole-genome sequencing and Rif-runout data. The analysis and code part consists of code and output from the analysis and post-processing.
DOI: 10.17044/scilifelab.22188583
title: Raw Expression Counts

description: Raw (unnormalized ) count data from Ampliseq Whole Transcriptome analyses of neuroblastoma samples, before and after chemotherapy. RNA was extracted from formalin fixed, paraffin embedded tissue blocks with standard methods and sequenced with Ion Torrent technology using the Ampliseq Whole Transcriptome assay. The raw data was processed through the standard Ion Torrent pipeline to generate raw counts for each transcript included in the Whole Transcriptome Assay.
DOI: 10.17044/scilifelab.22193854
title: Whole-genome sequencing in B-cell lymphomas for circulating tumor DNA analysis by multiplex digital PCR for disease monitoring

description: WGS data of paired tumor and normal samples in 9 patients (6 diffuse large B-cell lymphomas, 1 transformed follicular lymphoma and 2 follicular lymphoma) with a median depth of 37X (range: 27-50X). 
The study was approved by the Stockholm Regional Ethical committee (2017/2538-31) and conducted in accordance with the Declaration of Helsinki. Written informed consent  was obtained from the patients. 
The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic fresh frozen lymph node biopsies and matching whole blood for germline analysis. Sequencing was performed on a NovaSeq 6000 system (Illumina) using paired-end 150 bp readout, aiming at 300 M paired reads.  Pre-processing of raw FASTQ files and variant calling was performed by Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (BALSAMIC) version 10.0.2.
<br>
<strong>Data Access Statement</strong>
<br>
The WGS dataset are only to be used for academic research purposes at advancing the understanding of genetic factors in the pathogenesis of B-cell lymphomas. Applications, including those aimed at method development and bioinformatics, would only be considered as acceptable if proof of approved ethical consent is provided. Access requests should be sent to the email adress below.
DOI: 10.7483/opendata.cms.h80x.vn2s
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.22139918
title: Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

description: Bacteria replicate the genome on average once per generation, irrespective of growth condition-dependent changes in generation time and cell size. The strategy appears to be to initiate replication in a narrow chromosome-to-size ratio interval for each growth condition. To investigate how <em>Escherichia coli </em>accurately compares its size to the number of chromosomes, we perturbed some of the mechanisms proposed to achieve this precision and monitored how replication initiation was affected with time-lapse single-cell fluorescence microscopy. We found that the regulatory inactivation of DnaA-ATP (RIDA) mechanism, which converts the replication initiation molecule DnaA to its inactive form in proportion to the number of chromosomes, was the most important factor and that other previously described mechanisms have a less critical role. 
<br>
This dataset contains the raw data, analysis and code needed to generate the figures presented in the paper. The raw data consists of microscopy images, growth rate measurements, RT-qPCR, whole-genome sequencing and Rif-runout data. The analysis and code part consists of code and output from the analysis and post-processing.
DOI: 10.17044/scilifelab.22193854.v1
title: Whole-genome sequencing in B-cell lymphomas for circulating tumor DNA analysis by multiplex digital PCR for disease monitoring

description: WGS data of paired tumor and normal samples in 9 patients (6 diffuse large B-cell lymphomas, 1 transformed follicular lymphoma and 2 follicular lymphoma) with a median depth of 37X (range: 27-50X). 
The study was approved by the Stockholm Regional Ethical committee (2017/2538-31) and conducted in accordance with the Declaration of Helsinki. Written informed consent  was obtained from the patients. 
The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic fresh frozen lymph node biopsies and matching whole blood for germline analysis. Sequencing was performed on a NovaSeq 6000 system (Illumina) using paired-end 150 bp readout, aiming at 300 M paired reads.  Pre-processing of raw FASTQ files and variant calling was performed by Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (BALSAMIC) version 10.0.2.
<br>
<strong>Data Access Statement</strong>
<br>
The WGS dataset are only to be used for academic research purposes at advancing the understanding of genetic factors in the pathogenesis of B-cell lymphomas. Applications, including those aimed at method development and bioinformatics, would only be considered as acceptable if proof of approved ethical consent is provided. Access requests should be sent to the email adress below.
DOI: 10.15468/dl.d9zyu9
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Material citation, Specimen, Living Specimen)",
 "Continent is one of (North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Negaprion brevirostris (Poey, 1868)"
 ]
}

 The dataset includes 133 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071208-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.cms.v6o1.x6oz
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22188583.v1
title: Raw Expression Counts

description: Raw (unnormalized ) count data from Ampliseq Whole Transcriptome analyses of neuroblastoma samples, before and after chemotherapy. RNA was extracted from formalin fixed, paraffin embedded tissue blocks with standard methods and sequenced with Ion Torrent technology using the Ampliseq Whole Transcriptome assay. The raw data was processed through the standard Ion Torrent pipeline to generate raw counts for each transcript included in the Whole Transcriptome Assay.
DOI: 10.17044/scilifelab.22225942
title: Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS)

description: Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS)
This dataset contain normalised MFI values from an affinity proteomics screenings in Citrate plasma and EDTA plasma from 96 individuals with suspected acute venous thrombosis. 
The data is disaggregated on individual level with information about sex.
Data linked to other phenotype information has been deposited separately with restricted access available upon request.
DOI: 10.17044/scilifelab.22225942.v1
title: Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS)

description: Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS)
This dataset contain normalised MFI values from an affinity proteomics screenings in Citrate plasma and EDTA plasma from 96 individuals with suspected acute venous thrombosis. 
The data is disaggregated on individual level with information about sex.
Data linked to other phenotype information has been deposited separately with restricted access available upon request.
DOI: 10.7483/opendata.cms.xej6.hnfa
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.22226350.v1
title: Elevated plasma Complement Factor H Related 5 Protein is associated with venous thromboembolism

description: The study is based on 6 different cohorts and case control studies of patients with venous thromboembolism (VTE). The six cohorts are briefly as described below: 
VEBIOS ER, Swedish acute VTE cohort including 48 cases and 48 controls. 
DFW. Swedish acute VTE cohort with 54 cases/146 controls.
FARIVE: French cohort including 582 patients recruited druing initiation of treatment for VTE and 576 hospital-based controls.
VEBIOS Coagulation, Swedish cohort, with 144 cases followed after ending treatment of VTE and 140 controls population-based recluted.
RETROVE, Spanish cohort of 308 cases and 360 controls. Cases were recruted after ending VTE treatment.
MARTHA, French cohort, Patiens with prior VTE. n=774.
<br>
The datasets include anonymized participant-level data generated from analyses of plasma samples from the included cohort and case-control studies, including plasma affinity proteomics data, absolute protein quantifications, Thrombin Generation Potential (TGP) measurements, together with clinical chemistry data and clinical information used in the analyses described in the paper.<br>

The data can be made available for validation purposes upon reasonable request (jacob.odeberg@scilifelab.se)
A reasonable request should contain:
1) Name of PI and host organisation
2) Contact details
3) Scientific purpose of data access request
4) Commitment to inform when the data has been used in a publication
5) Commitment not to host or share the data outside the requesting organisation
6) Statement of non-commercial use of data
DOI: 10.7483/opendata.cms.8unv.t2yg
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.15468/dl.6pr2s8
title: Occurrence Download

description: A dataset containing 461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isomira antennata (Panzer, 1798)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 461 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071207-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.cms.ndg6.drgc
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.sagr.9zqr
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.1dgr.dlvq
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.22269211
title: Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis

description: Dataset from Geroldinger-Simic, M.; Bayati, S.; Pohjanen, E.; et al. Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis. Int J Mol Sci. Accepted on March 2023
<br>
Abstract:  Systemic sclerosis (SSc) is a rare autoimmune systemic disease that leads to decreased survival and quality of life due to fibrosis, inflammation, and vascular damage in the skin and/or vital organs. Early diagnosis is crucial for clinical benefit in SSc patients. Our study aimed to identify autoantibodies in the plasma of SSc patients that are associated with fibrosis in SSc. Initially, we performed a proteome-wide screening on sample pools from SSc patients by untargeted autoantibody screening on a planar antigen array (including 42,000 antigens representing 18,000 unique proteins). The selection was complemented with proteins reported in the literature in the context of SSc. A targeted antigen bead array was then generated with protein fragments representing the selected proteins and used to screen 55 SSc plasma samples and 52 matched controls. We found eleven autoantibodies with a higher prevalence in SSc patients than in controls, eight of which were associated with fibrosis. Combining these autoantibodies in a panel could lead to the subgrouping of SSc patients with fibrosis. Anti-Phosphatidylinositol-5-phosphate 4-kinase type 2 beta (PIP4K2B)- and anti-AKT Serine/Threonine Kinase 3 (AKT3)-antibodies should be further explored to confirm their association with skin and lung fibrosis in SSc patients. 
<br>
This dataset contains relative continuous as well as binarized autoantibody data, with associated clinical data on the presence of currently clinically available autoantibody biomarkers (e.g. anti-Scl70 and anti-centromere antibodies) and symptomes (e.g. mRSS score, lung fibrosis, digital ulcers, Raynauds, reflux, sicca). 
<br>
<strong>Data Access Statement</strong>
These data constitute sensitive personal information that fall under the GDPR. Therefore, access to data and related code is restricted. The data can be made available for validation purposes, upon reasonable request and in accordance with GDPR.<br>
<br>
A reasonable request should contain:<br>
1) Name of PI and host organisation<br>
2) Contact details<br>
3) Scientific purpose of data access request<br>
4) Commitment to inform when the data has been used in a publication<br>
5) Commitment not to host or share the data outside the requesting organisation<br>
6) Statement of non-commercial use of data
DOI: 10.17044/scilifelab.22269211.v1
title: Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis

description: Dataset from Geroldinger-Simic, M.; Bayati, S.; Pohjanen, E.; et al. Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis. Int J Mol Sci. Accepted on March 2023
<br>
Abstract:  Systemic sclerosis (SSc) is a rare autoimmune systemic disease that leads to decreased survival and quality of life due to fibrosis, inflammation, and vascular damage in the skin and/or vital organs. Early diagnosis is crucial for clinical benefit in SSc patients. Our study aimed to identify autoantibodies in the plasma of SSc patients that are associated with fibrosis in SSc. Initially, we performed a proteome-wide screening on sample pools from SSc patients by untargeted autoantibody screening on a planar antigen array (including 42,000 antigens representing 18,000 unique proteins). The selection was complemented with proteins reported in the literature in the context of SSc. A targeted antigen bead array was then generated with protein fragments representing the selected proteins and used to screen 55 SSc plasma samples and 52 matched controls. We found eleven autoantibodies with a higher prevalence in SSc patients than in controls, eight of which were associated with fibrosis. Combining these autoantibodies in a panel could lead to the subgrouping of SSc patients with fibrosis. Anti-Phosphatidylinositol-5-phosphate 4-kinase type 2 beta (PIP4K2B)- and anti-AKT Serine/Threonine Kinase 3 (AKT3)-antibodies should be further explored to confirm their association with skin and lung fibrosis in SSc patients. 
<br>
This dataset contains relative continuous as well as binarized autoantibody data, with associated clinical data on the presence of currently clinically available autoantibody biomarkers (e.g. anti-Scl70 and anti-centromere antibodies) and symptomes (e.g. mRSS score, lung fibrosis, digital ulcers, Raynauds, reflux, sicca). 
<br>
<strong>Data Access Statement</strong>
These data constitute sensitive personal information that fall under the GDPR. Therefore, access to data and related code is restricted. The data can be made available for validation purposes, upon reasonable request and in accordance with GDPR.<br>
<br>
A reasonable request should contain:<br>
1) Name of PI and host organisation<br>
2) Contact details<br>
3) Scientific purpose of data access request<br>
4) Commitment to inform when the data has been used in a publication<br>
5) Commitment not to host or share the data outside the requesting organisation<br>
6) Statement of non-commercial use of data
DOI: 10.17044/scilifelab.22270225
title: Metagenomic dataset from Swedish urban lakes

description: We release metagenomic data of seven urban, eutrophic Swedish lakes that have been extensively studied and characterized in terms of biogeochemistry. Here we provide the supplementary tables and the full set of metagenome-assembled genomes of 17 metagenomic samples.
- We have 10 metagenomic samples from Lake Mälaren which is the third largest lake in Sweden and serves as the main drinking water supply to ~1.5 million residents in Stockholm and neighboring cities. This dataset is the first insight into the bacterial dynamics of Lake Mälaren during the summer seasonal gradient (early July – late August 2021).
- We sampled two additional lakes (Trehoringen and Langsjön) in Uppsala to compare summer microbial communities in lakes in Central Sweden.
- Additionally, we sequenced, assembled and binned microbial communities in five Swedish lakes in the urban Stockholm-Uppsala region from 2002 that were previously characterized using older techniques (Eiler and Bertilsson, 2004). These five highly eutrophic lakes have a long history of seasonal cyanobacterial blooms in the summer (Eiler and Bertilsson, 2004).
Our goal was to collect and sequence data that could be used to generate hypothesis and preliminary view of microbial community or urban lakes around Stockholm with special emphasis on Lake Mälaren which proved drinking water to millions of people. In these data we release 17 shot-gun metagenomes in the European Nucleotide Archive (ENA) and are accessible under project number PRJEB54817. Moreover, in this repository we provide the 2378 MAGs that include the 514 species representative genomes (SRG, calculated &lt;95% average nucleotide identity - ANI).
Finally, here you also can find the 4 supplementary tables that include the following information.
· Table S1. Sample metadata
· Table S2. Metagenomic assembly statistics (QUAST)
· Table S3. List of metagenome assembled genomes (MAGs), checkM statistics and GTDB taxonomic classification. Dereplicated species representative genomes are marked with x
· Table S4. Species representative genomes (SRGs) abundance in copies per million reads
DOI: 10.7483/opendata.cms.mzdh.t29h
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.kmtq.hhs0
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.0n6i.p84m
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22284709.v1
title: Atlas of 5'P mRNA decay in bacteria

description: Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an <em>in vivo</em> single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.
<br>
Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. <em>NAR Genomics and Bioinformatics</em>, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099
DOI: 10.7483/opendata.cms.d8cl.l4kx
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.mnju.e42g
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22226350
title: Elevated plasma Complement Factor H Related 5 Protein is associated with venous thromboembolism

description: The study is based on 6 different cohorts and case control studies of patients with venous thromboembolism (VTE). The six cohorts are briefly as described below: 
VEBIOS ER, Swedish acute VTE cohort including 48 cases and 48 controls. 
DFW. Swedish acute VTE cohort with 54 cases/146 controls.
FARIVE: French cohort including 582 patients recruited druing initiation of treatment for VTE and 576 hospital-based controls.
VEBIOS Coagulation, Swedish cohort, with 144 cases followed after ending treatment of VTE and 140 controls population-based recluted.
RETROVE, Spanish cohort of 308 cases and 360 controls. Cases were recruted after ending VTE treatment.
MARTHA, French cohort, Patiens with prior VTE. n=774.
<br>
The datasets include anonymized participant-level data generated from analyses of plasma samples from the included cohort and case-control studies, including plasma affinity proteomics data, absolute protein quantifications, Thrombin Generation Potential (TGP) measurements, together with clinical chemistry data and clinical information used in the analyses described in the paper.<br>

The data can be made available for validation purposes upon reasonable request (jacob.odeberg@scilifelab.se)
A reasonable request should contain:
1) Name of PI and host organisation
2) Contact details
3) Scientific purpose of data access request
4) Commitment to inform when the data has been used in a publication
5) Commitment not to host or share the data outside the requesting organisation
6) Statement of non-commercial use of data
DOI: 10.7483/opendata.cms.8uks.hg1g
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.udvn.zten
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.r42q.6zo6
title: /TprimeBToTH_TLep_Hbb_LH_MT3000_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM