cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.13229168.v2
title: 5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

description: Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in <i>Saccharomyces cerevisiae. </i>Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200<br>Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using <i>fivepseq</i> pipeline http://pelechanolab.com/software/fivepseq/<br><b>Related manuscript abstract:</b><br>Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the <i>rpl3</i>[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.<br><b>Raw data:</b>Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession number GSE114899 and GSE151632<br><br>
DOI: 10.7483/opendata.cms.7lr8.hjf5
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.13280867
title: Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds

description: <strong>Abstract</strong>
Increased knowledge of the evolution of molecular changes in neurodegenerative disorders such as Alzheimer’s disease (AD) is important for the understanding of disease pathophysiology and also crucial to be able to identify and validate disease biomarkers. While several biological changes that occur early in the disease development have already been recognised, the need for further characterization of the pathophysiological mechanisms behind AD still remains.
<br>
In this study, we investigated cerebrospinal fluid (CSF) levels of 104 proteins in 307 asymptomatic 70-year-olds from the H70 Gothenburg Birth Cohort Studies using a multiplexed antibody-based technology.
<br>
The protein levels were first correlated with the core AD CSF biomarker concentrations of total tau, phospho-tau and Aβ42 in all individuals. Sixty-three proteins showed significant correlations with either total tau, phospho-tau or Aβ42. Thereafter, individuals were divided based on CSF Aβ42/Aβ40 ratio and Clinical Dementia Rating (CDR) score to determine if early changes in pathology and cognition had an effect on the correlations. We compared the associations of the analysed proteins to CSF markers between groups and found 33 proteins displaying significantly different associations for amyloid-positive individuals and amyloid negative individuals, as defined by the CSF Aβ42/Aβ40 ratio. No differences in the associations could be seen for individuals divided by CDR score.
<br>
We identified a series of transmembrane proteins, proteins associated to or anchored to the plasma membrane, and proteins involved in or connected to synaptic vesicle transport that were associated with CSF biomarkers of amyloid and tau pathology in AD. Further studies are needed to explore their role in AD pathophysiology.
<br>
<strong>Data Access Statement</strong>
The dataset contains relative protein levels as well as CSF concentrations of amyloid beta and tau which constitutes sensitive personal information that fall under GDPR. Therefore, access to data and related code is restricted. The data can be made available upon reasonable request, in accordance with GDPR and other regulations regarding data sharing.
<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
<br>
DOI: 10.7483/opendata.cms.vvsf.bgir
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.6084/m9.figshare.25422940
title: Dataset Kidney Panel Variants 2024 #20-25

description: The dataset contains all the variants identified after WES and filtering by a kidney panel.
DOI: 10.6084/m9.figshare.25422940.v1
title: Dataset Kidney Panel Variants 2024 #20-25

description: The dataset contains all the variants identified after WES and filtering by a kidney panel.
DOI: 10.17044/scilifelab.13293344
title: Browsable TIF-Seq2 tracks from K562 after imatinib treatment

description: Browsable dataset containing transcript boundaries for the manuscript:<br>Jingwen Wang, Bingnan Li, Sueli Marques, Lars M Steinmetz, Wu Wei, Vicent Pelechano, TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes, Nucleic Acids Research, Volume 48, Issue 18, 09 October 2020, Page e104, https://doi.org/10.1093/nar/gkaa691 <br>The alignment files contains sequences of K562 cells using TIF-Seq2 method. The sequencing reads were aligned to the human reference genome hg38. Each read pair represents the boundary of an individual transcript. The first reads in pairs are 5' ends, while the second reads in pairs are 3' ends. The alignment files can be loaded into IGV for visualization. You can set up view as pairs in the alignment track.<br>Source code for the associated manuscript is available from GitHub at https://github.com/jingwen/TIFseq2<br>Raw data is deposited at GEO with access code GSE140912<br>
DOI: 10.17044/scilifelab.13293344.v1
title: Browsable TIF-Seq2 tracks from K562 after imatinib treatment

description: Browsable dataset containing transcript boundaries for the manuscript:<br>Jingwen Wang, Bingnan Li, Sueli Marques, Lars M Steinmetz, Wu Wei, Vicent Pelechano, TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes, Nucleic Acids Research, Volume 48, Issue 18, 09 October 2020, Page e104, https://doi.org/10.1093/nar/gkaa691 <br>The alignment files contains sequences of K562 cells using TIF-Seq2 method. The sequencing reads were aligned to the human reference genome hg38. Each read pair represents the boundary of an individual transcript. The first reads in pairs are 5' ends, while the second reads in pairs are 3' ends. The alignment files can be loaded into IGV for visualization. You can set up view as pairs in the alignment track.<br>Source code for the associated manuscript is available from GitHub at https://github.com/jingwen/TIFseq2<br>Raw data is deposited at GEO with access code GSE140912<br>
DOI: 10.17044/scilifelab.13297784
title: Distinct developmental pathways from blood monocytes generate human lung macrophage diversity

description: <b>RNA-sequencing data sets</b>(1) Single-cell RNA-sequencing data of human lung myeloid cells from
MISTRG mice on day 21 post-transplantation with human CD34<sup>+</sup> cells

 

(2) Single-cell RNA-sequencing data of human lung myeloid cells from
MISTRG mice on day 36 post-transplantation with human CD34<sup>+</sup> cells

 

(3)
Bulk RNA-sequencing data of human intravascular monocytes, intravascular
macrophages, and extravascular macrophages from the lungs of MISTRG mice
engrafted with human CD34<sup>+</sup> cells<br><b>Data collection methods</b>See Resource DOI<br><br><b>Publication abstract</b>The study of human macrophages and their ontogeny is an important
unresolved issue. Here, we use a humanized mouse model expressing human
cytokines to dissect the development of lung macrophages from human
hematopoiesis in vivo. Human CD34+ hematopoietic stem and progenitor cells
(HSPCs) generated three macrophage populations, occupying separate anatomical
niches in the lung. Intravascular cell labeling, cell transplantation, and
fate-mapping studies established that classical CD14+ blood monocytes derived
from HSPCs migrated into lung tissue and gave rise to human interstitial and
alveolar macrophages. In contrast, non-classical CD16+ blood monocytes
preferentially generated macrophages resident in the lung vasculature
(pulmonary intravascular macrophages). Finally, single-cell RNA-sequencing defined
intermediate differentiation stages in human lung macrophage development from
blood monocytes. This study identifies distinct developmental pathways from circulating monocytes to lung macrophages and reveals how cellular
origin contributes to human macrophage identity, diversity, and localization in
vivo.<br>
DOI: 10.7483/opendata.cms.qxh9.s7hy
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.13297784.v1
title: Distinct developmental pathways from blood monocytes generate human lung macrophage diversity

description: <b>RNA-sequencing data sets</b>(1) Single-cell RNA-sequencing data of human lung myeloid cells from
MISTRG mice on day 21 post-transplantation with human CD34<sup>+</sup> cells

 

(2) Single-cell RNA-sequencing data of human lung myeloid cells from
MISTRG mice on day 36 post-transplantation with human CD34<sup>+</sup> cells

 

(3)
Bulk RNA-sequencing data of human intravascular monocytes, intravascular
macrophages, and extravascular macrophages from the lungs of MISTRG mice
engrafted with human CD34<sup>+</sup> cells<br><b>Data collection methods</b>See Resource DOI<br><br><b>Publication abstract</b>The study of human macrophages and their ontogeny is an important
unresolved issue. Here, we use a humanized mouse model expressing human
cytokines to dissect the development of lung macrophages from human
hematopoiesis in vivo. Human CD34+ hematopoietic stem and progenitor cells
(HSPCs) generated three macrophage populations, occupying separate anatomical
niches in the lung. Intravascular cell labeling, cell transplantation, and
fate-mapping studies established that classical CD14+ blood monocytes derived
from HSPCs migrated into lung tissue and gave rise to human interstitial and
alveolar macrophages. In contrast, non-classical CD16+ blood monocytes
preferentially generated macrophages resident in the lung vasculature
(pulmonary intravascular macrophages). Finally, single-cell RNA-sequencing defined
intermediate differentiation stages in human lung macrophage development from
blood monocytes. This study identifies distinct developmental pathways from circulating monocytes to lung macrophages and reveals how cellular
origin contributes to human macrophage identity, diversity, and localization in
vivo.<br>
DOI: 10.17044/scilifelab.12811997
title: Snat10 Knockout Mice Cortical Neuronal Cells (ImageXpress XLS Example Images)

description: Image set collected in the Spjuth Lab (https://pharmb.io/), used as a test dataset for the HASTE software tools, and referenced in associated publications.<br>The images are of Snat10 knockout mice cortical neuronal cells, grown for 7 days and treated with either hydrogen peroxide or glutamate.<br>In total, there are 2699 TIFF images, organized by wavelength.<br>Images were taken with an ImageXpress XLS, at the Spjuth Lab.<br>All the archives decompress into this path:./181214-KOday7-40X-H2O2-Glu/2018-12-14/9/*.tif
DOI: 10.17044/scilifelab.13325822
title: Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing

description: This dataset includes whole genome sequencing (WGS) data of 20 diagnostic, and 20 remission samples from 20 children/adolescents with acute myeloid leukemia (AML), treated at the Departments of Pediatrics at Lund and Linköping University Hospitals between 1994 and 2016. The median age of the patients was 8 years (range 0-17 years) and the female/male ratio was 1:1. DNA was extracted from diagnostic bone marrow (BM; n = 17)/peripheral blood (PB; n = 3) samples, remission BM (n = 15)/PB (n = 5), and from two BM relapses. Construction of libraries, using the TruSeq Nano DNA sample preparation kit (Illumina, San Diego, CA, USA) on 100 ng DNA, and massively parallel sequencing were performed by BGI Tech Solutions (Hong Kong). The WGS (Illumina HiSeqX) reached an average sequencing depth of 30-42x/sample (median 33x), with 2x 150 bp read length. <br><br>
DOI: 10.7483/opendata.cms.w5x6.fzz4
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.13325822.v1
title: Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing

description: This dataset includes whole genome sequencing (WGS) data of 20 diagnostic, and 20 remission samples from 20 children/adolescents with acute myeloid leukemia (AML), treated at the Departments of Pediatrics at Lund and Linköping University Hospitals between 1994 and 2016. The median age of the patients was 8 years (range 0-17 years) and the female/male ratio was 1:1. DNA was extracted from diagnostic bone marrow (BM; n = 17)/peripheral blood (PB; n = 3) samples, remission BM (n = 15)/PB (n = 5), and from two BM relapses. Construction of libraries, using the TruSeq Nano DNA sample preparation kit (Illumina, San Diego, CA, USA) on 100 ng DNA, and massively parallel sequencing were performed by BGI Tech Solutions (Hong Kong). The WGS (Illumina HiSeqX) reached an average sequencing depth of 30-42x/sample (median 33x), with 2x 150 bp read length. <br><br>
DOI: 10.17044/scilifelab.13564364
title: Dataset for "Serological and molecular study of Crimean-Congo hemorrhagic fever virus in cattle from selected districts in Uganda" _serology_25012021

description: <br>DATASET This dataset presented is a summary of information about the animals and test results that are reported in the Manuscript, ‘Serological and Molecular Study of Crimean-Congo Hemorrhagic Fever Virus in cattle from selected districts in Uganda’. Below is an explanation text on some of the data variables and acronyms found in the file. A: BIODATA WORKSHEET contains information about number, code, district, sub county, parish, village and GPS location of where study samples were collected, sex of samples animal breed, age, weight, BCS, health status, rectal temperature and tick burden estimate.<b>B: ELISA WORKSHEET contains ELISA results for 500 samples as assessed with two different assays, the In-house anti−CCHFV specific immunoglobulin g (IgG) ELISA and IDvet kit ID Screen® CCHF Double Antigen Multi-species ELISA.</b>C: IFA AND PCR WORKSHEET contains RT-PCR performed in order to detect any CCHF viral particles in the serum samples of 37 samples. A summary of categories of samples (selected according to their individual results from the IDVet and In-house assay) and their Unique identification numbers that were tested for both IFA (Immunofluorescent assay) and PCR (Polymerase Chain Reaction). The results for each sample is indicated. <b>Title: Serological and molecular study of Crimean-Congo hemorrhagic fever virus in cattle from selected districts in Uganda</b><br><b><br></b>Journal of Virological Methods, in press 27 January 2021https://doi.org/10.1016/j.jviromet.2021.114075<br><br><br><b>Abstract </b>

<b>Background: </b>Crimean-Congo Hemorrhagic Fever (CCHF) is a severe tick-borne viral
hemorrhagic disease caused by Crimean-Congo Hemorrhagic Fever Virus (CCHFV)
that poses serious public health challenges in many parts of Africa, Europe and
Asia.

<b>Methods:</b> We examined 500 cattle sera samples from five districts for CCHFV antibodies
using in-house and commercially available (IDVet) ELISA, Immunofluorescent
assay (IFA) and Real-time polymerase chain reaction (RT-PCR).

<b>Results:</b> 500 cattle (73.8% females) were analyzed; CCHFV seropositivity was
12.6% (n = 63) and 75.0% (n = 375) with the in-house and IDVet ELISAs,
respectively. Seropositivity was associated with geographical location, increasing
age, being female, and having a higher tick burden. Twentyfour out of the 37 (64.8%)
were seropositive for CCHFV using IFA and negative for virus on RT-PCR. The IFA results were more comparable to IDVet (κ<sub>coefficient</sub>
= 0.88, p = &lt;0.01) than to in-house (κ<sub>coefficient</sub> = 0.32, p =
0.02). 

<b>Conclusions:</b> Our study confirmed the presence and high prevalence of anti-CCHF antibodies
in cattle based on three methods from all the five study districts, confirming
presence and exposure of CCHFV. Given
the zoonotic potential for CCHFV, we recommend a multidisciplinary public
health surveillance and epidemiology of CCHFV in both animals and humans
throughout the country.
DOI: 10.17044/scilifelab.13564364.v1
title: Dataset for "Serological and molecular study of Crimean-Congo hemorrhagic fever virus in cattle from selected districts in Uganda" _serology_25012021

description: <br>DATASET This dataset presented is a summary of information about the animals and test results that are reported in the Manuscript, ‘Serological and Molecular Study of Crimean-Congo Hemorrhagic Fever Virus in cattle from selected districts in Uganda’. Below is an explanation text on some of the data variables and acronyms found in the file. A: BIODATA WORKSHEET contains information about number, code, district, sub county, parish, village and GPS location of where study samples were collected, sex of samples animal breed, age, weight, BCS, health status, rectal temperature and tick burden estimate.<b>B: ELISA WORKSHEET contains ELISA results for 500 samples as assessed with two different assays, the In-house anti−CCHFV specific immunoglobulin g (IgG) ELISA and IDvet kit ID Screen® CCHF Double Antigen Multi-species ELISA.</b>C: IFA AND PCR WORKSHEET contains RT-PCR performed in order to detect any CCHF viral particles in the serum samples of 37 samples. A summary of categories of samples (selected according to their individual results from the IDVet and In-house assay) and their Unique identification numbers that were tested for both IFA (Immunofluorescent assay) and PCR (Polymerase Chain Reaction). The results for each sample is indicated. <b>Title: Serological and molecular study of Crimean-Congo hemorrhagic fever virus in cattle from selected districts in Uganda</b><br><b><br></b>Journal of Virological Methods, in press 27 January 2021https://doi.org/10.1016/j.jviromet.2021.114075<br><br><br><b>Abstract </b>

<b>Background: </b>Crimean-Congo Hemorrhagic Fever (CCHF) is a severe tick-borne viral
hemorrhagic disease caused by Crimean-Congo Hemorrhagic Fever Virus (CCHFV)
that poses serious public health challenges in many parts of Africa, Europe and
Asia.

<b>Methods:</b> We examined 500 cattle sera samples from five districts for CCHFV antibodies
using in-house and commercially available (IDVet) ELISA, Immunofluorescent
assay (IFA) and Real-time polymerase chain reaction (RT-PCR).

<b>Results:</b> 500 cattle (73.8% females) were analyzed; CCHFV seropositivity was
12.6% (n = 63) and 75.0% (n = 375) with the in-house and IDVet ELISAs,
respectively. Seropositivity was associated with geographical location, increasing
age, being female, and having a higher tick burden. Twentyfour out of the 37 (64.8%)
were seropositive for CCHFV using IFA and negative for virus on RT-PCR. The IFA results were more comparable to IDVet (κ<sub>coefficient</sub>
= 0.88, p = &lt;0.01) than to in-house (κ<sub>coefficient</sub> = 0.32, p =
0.02). 

<b>Conclusions:</b> Our study confirmed the presence and high prevalence of anti-CCHF antibodies
in cattle based on three methods from all the five study districts, confirming
presence and exposure of CCHFV. Given
the zoonotic potential for CCHFV, we recommend a multidisciplinary public
health surveillance and epidemiology of CCHFV in both animals and humans
throughout the country.
DOI: 10.7483/opendata.cms.iho5.pgz5
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.15468/dl.mszmdm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Pseudohydrosme"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071186-241126133413365/datasets/export for details.
DOI: 10.17044/scilifelab.13567355.v1
title: COMMUNITY study

description: Datasets from COMMUNITY study including 2149 healthcare workers. Longitudinal cohort study. Data include1. Data from serological analysis HCW n=2149 and patients n=118 at baseline and HCW n=1974 and patients n=59 at four-month follow-up.Raw data from IgG antibodies against various epitopes on the SARS-CoV-2 virus.<br><br>2. Raw data from collected self-report questionnaire (N=2149) investigating predefined prior symptoms compatible with COVID-19 since 1 January 2020, occupation, work location and self-reported exposure to patients infected with COVID-19 prior to blood sampling. The questionnaire consisted of 11 predefined symptoms (fever, headache, anovsmia, ageusia, cough, malaise, common cold, abdominal pain, sore throat, shortness of breath) including the alternative “no ongoing or prior symptoms since 1 January 2020”<br>AbstractThe COMMUNITY study is a large longitudinal cohort study including 2149 healthcare workers and 118 CPVOD-19 patients. The aim is to obtain a deeper understanding of the generation and dynamics of SARS-CoV-2 immune memory (humoral and cellular). We also aim to map and investigate virus and immune-mediated persistent symptomatology, so called long-COVID, and susceptibility/resistance to SARS-CoV-2. Study inclusion was initiated April 2020, and serial blood samples are obtained from the same 2149 individuals and patients who survived every four months. Notably, a large portion of HCW study participants (19%) had been infected with COVID-19 at study inclusion, and the vast majority reported no or mild symptoms, thus representing the portion of society generating the most transmission. The cohort, including an extensive database, furthermore allows for a comprehensive mapping of long-COVID which can be used to help target early interventions aimed at capturing, preventing and treating this condition.
DOI: 10.7483/opendata.cms.caqe.vrz8
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH500_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM