cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.21378279
title: Spatially-resolved chromatin accessibility and transcriptomic profiling of human breast cancer

description: Human breast cancer OMICs data generated for the publication "Solid phase capture and profiling of open chromatin by spatial ATAC"<br>

<strong>Abstract from the publication:</strong>
Current methods for epigenomic profiling are limited in the ability to obtain genome wide information with spatial resolution. Here we introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
<br>
<strong>Dataset description</strong>
The dataset includes spatially-resolved chromatin accessibility profiling performed on three fresh-frozen tissue sections of HER2+ breast cancer. We provide raw data in the form of fastq files, along with processed feature barcode matrices, metadata, and photomicrographs of the tissue slices. Additionally the dataset contains spatially-resolved gene expression profiling of tissue sections from the same specimen. For this too, we provide raw and processed data, along with the metadata information.
<br>
Spatial transcriptomics data were generated using 10X Genomics' Visium platform, while spatial ATAC data were created using a method introduced in our publication, which relies on an analogous workflow. Samples were sequenced on Illumina Nextseq 550 or 2000 and raw data were processed with CellRanger Gene Expression or ATAC-seq pipelines.
<br>
To apply for conditional access to the dataset, please contact datacentre@scilifelab.se.
<br>
<br>
DOI: 10.7483/opendata.cms.bvcx.w680
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.g7fa.jcc5
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.21407402
title: Multi-site assessment of reproducibility in high-content live cell imaging data

description: This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data". 
<br>
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental chamber. The experiment was performed by 3 labs, 3 person in each lab, 3 independent experiments by each person, 3 technical replicates in each experiment, and two conditions (control and ROCK inhibition) for each technical repliates. 
<br>
The Data processing and analysis-2D.rar file contains the Matlab, CellProfiler, ImageJ, and R pipelines and scripts used in this study to process, quantify, and analyze the images. Detailed procedure could be found in the "Image processing and analysis procedures.txt" file within this .rar file.
<br>
The 3D Image data from Lab 1.zip and 3D Image data from Lab 2.zip contain the raw images and the quantified results of the 3D migration assay from Lab 1 and Lab 2, respectively. The experiment was performed with HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry embedded in 2.5mg/ml or 6mg/ml collagen I gels. The invasion of the cells from 3D spheroid was recorded with confocal microscopy 24 h after seeding. The experiment was performed by 2 labs, 3 independent experiments in each lab, 3 technical replicates in each experiment, and two conditions (2.5 mg/ml and 6 mg/ml of collagen I) for each technical repliates. 
<br>
The Meta data of the 3D experiment.zip contains the meta data of the 3D image data from Lab 1 (Radboudumc) and Lab 2 (Crick) as well as the software to read the meta data. After unzipping, ISAcreator program should be used to read the ISAfiles of Lab 1 or Lab 2.
<br>
The Fiji Plugins and parameters for 3D image data analysis.rar contains the Fiji plugins and also the parameters used during the 3D image data analysis.
<br>
The 3D Data Analysis Scripts.rar contains the R scripts used in this study to analyze the 3D data set, as well as the quantified results needed by the R scripts.
<br>
The Supplementary Materials 2-8.rar contains 2D experimental protocol (supplementary materials 2-4), 2D experimental survey (supplementary materials 3), and 3D experimental and image analysis protocols (supplementary materials 5-8) that are used in this study.
<br>
We encourage reuse using the same CC BY 4.0 License.
DOI: 10.7483/opendata.cms.ued0.r9cc
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH500_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.21407402.v2
title: Multi-site assessment of reproducibility in high-content live cell imaging data

description: This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data". 
<br>
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental chamber. The experiment was performed by 3 labs, 3 person in each lab, 3 independent experiments by each person, 3 technical replicates in each experiment, and two conditions (control and ROCK inhibition) for each technical repliates. 
<br>
The Data processing and analysis-2D.rar file contains the Matlab, CellProfiler, ImageJ, and R pipelines and scripts used in this study to process, quantify, and analyze the images. Detailed procedure could be found in the "Image processing and analysis procedures.txt" file within this .rar file.
<br>
The 3D Image data from Lab 1.zip and 3D Image data from Lab 2.zip contain the raw images and the quantified results of the 3D migration assay from Lab 1 and Lab 2, respectively. The experiment was performed with HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry embedded in 2.5mg/ml or 6mg/ml collagen I gels. The invasion of the cells from 3D spheroid was recorded with confocal microscopy 24 h after seeding. The experiment was performed by 2 labs, 3 independent experiments in each lab, 3 technical replicates in each experiment, and two conditions (2.5 mg/ml and 6 mg/ml of collagen I) for each technical repliates. 
<br>
The Meta data of the 3D experiment.zip contains the meta data of the 3D image data from Lab 1 (Radboudumc) and Lab 2 (Crick) as well as the software to read the meta data. After unzipping, ISAcreator program should be used to read the ISAfiles of Lab 1 or Lab 2.
<br>
The Fiji Plugins and parameters for 3D image data analysis.rar contains the Fiji plugins and also the parameters used during the 3D image data analysis.
<br>
The 3D Data Analysis Scripts.rar contains the R scripts used in this study to analyze the 3D data set, as well as the quantified results needed by the R scripts.
<br>
The Supplementary Materials 2-8.rar contains 2D experimental protocol (supplementary materials 2-4), 2D experimental survey (supplementary materials 3), and 3D experimental and image analysis protocols (supplementary materials 5-8) that are used in this study.
<br>
We encourage reuse using the same CC BY 4.0 License.
DOI: 10.7483/opendata.cms.v3g6.by4f
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH500_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.21517710
title: Antibiotic perseverance increases the risk of resistance development

description: <strong>Experimental data description</strong>
All experiments performed are timelapse microscopy experiments. Each experiment contains two directories, one containing phase contrast images arranged by positions on the microfluidic device, and the other contains the analysis scripts. The 'Overview.csv' file contains a full description for the conditions in each experiment.
Experiments can be divided into 3 categories:
<br>
<strong>1. 4h exposure to various antibiotics (</strong><em><strong>E. coli</strong></em><strong>)</strong>
These are the main experiments within the paper where cells are exposed to various antibiotics at 1/8x, 1/4x, 1/2x and 1x MIC.  
a) EXP-21-BW5663_LB-1.zip (LB replicate 1)
b) EXP-22-BY2422_LB-2.zip (LB replicate 2)
c) EXP-21-BW5667_CAR-1.zip (CAR replicate 1)
d) EXP-22-BY1020_CAR-2.zip (CAR replicate 2)
e) EXP-21-BT2897_CRO-1.zip (CRO replicate 1)
f) EXP-22-BY2425_CRO-2.zip (CRO replicate 2)
g) EXP-21-BY1007_CHL-1.zip (CHL replicate 1)
h) EXP-22-BY1043_CHL-2.zip (CHL replicate 2)
i) EXP-21-BT2896_CIP-1.zip (CIP replicate 1)
j) EXP-22-BY2424_CIP-2.zip (CIP replicate 2)
k) EXP-21-BW5664_GEN-1.zip (GEN replicate 1)
l) EXP-22-BY1022_GEN-2.zip (GEN replicate 2)
m) EXP-21-BW5666_NIT-1.zip (NIT replicate 1)
n) EXP-22-BY2419_NIT-2.zip (NIT replicate 2)
o) EXP-21-BT2898_RIF-1.zip (RIF replicate 1)
p) EXP-21-BY1000_RIF-2.zip (RIF replicate 2)
q) EXP-21-BW5661_SPT-1.zip (SPT replicate 1)
r) EXP-21-BY1019_SPT-2.zip (SPT replicate 2)
s) EXP-21-BW5658_TET-1.zip (TET replicate 1)
t) EXP-22-BY2421_TET-1.zip (TET replicate 2)
<br>
<strong>2. 17h exposure to rifampicin (</strong><em><strong>E. coli</strong></em><strong>, </strong><em><strong>S. enterica</strong></em><strong>)</strong>
These experiments were performed to test the effect of long-term rifampicin exposure on <em>Escherichia coli</em> and <em>Salmonella enterica</em>.
a) EXP-21-BT2899.zip (<em>E. coli</em>)
b) EXP-21-BY1015.zip (<em>S. enterica</em>)
<br>
<strong>3. Growth in minimal medium (</strong><em><strong>E. coli</strong></em><strong>)</strong>
This experiment was performed to test how reducing the cellular growth rate (without antibiotics) affects the cell-to-cell growth heterogeneity.
a) EXP-22-BY2420.zip
<br>
<br>
<strong>Code</strong>
The 'codefolder' contains the ImAnalysis pipeline and the UNet used for image analysis. The scripts and parameter files to perform the image analysis are provided within each individual experiment folder. 
The 'Data_analysis' folder contains three directories: (i) 'Analysis_scripts', which contains the R scripts used for data analysis and figure generation; (ii) 'Raw_data', which contains the raw data underlying the figures in the paper; and (iii) 'Results', which is the output directory for the figures generated by the analysis scripts.
DOI: 10.17044/scilifelab.21517710.v1
title: Antibiotic perseverance increases the risk of resistance development

description: <strong>Experimental data description</strong>
All experiments performed are timelapse microscopy experiments. Each experiment contains two directories, one containing phase contrast images arranged by positions on the microfluidic device, and the other contains the analysis scripts. The 'Overview.csv' file contains a full description for the conditions in each experiment.
Experiments can be divided into 3 categories:
<br>
<strong>1. 4h exposure to various antibiotics (</strong><em><strong>E. coli</strong></em><strong>)</strong>
These are the main experiments within the paper where cells are exposed to various antibiotics at 1/8x, 1/4x, 1/2x and 1x MIC.  
a) EXP-21-BW5663_LB-1.zip (LB replicate 1)
b) EXP-22-BY2422_LB-2.zip (LB replicate 2)
c) EXP-21-BW5667_CAR-1.zip (CAR replicate 1)
d) EXP-22-BY1020_CAR-2.zip (CAR replicate 2)
e) EXP-21-BT2897_CRO-1.zip (CRO replicate 1)
f) EXP-22-BY2425_CRO-2.zip (CRO replicate 2)
g) EXP-21-BY1007_CHL-1.zip (CHL replicate 1)
h) EXP-22-BY1043_CHL-2.zip (CHL replicate 2)
i) EXP-21-BT2896_CIP-1.zip (CIP replicate 1)
j) EXP-22-BY2424_CIP-2.zip (CIP replicate 2)
k) EXP-21-BW5664_GEN-1.zip (GEN replicate 1)
l) EXP-22-BY1022_GEN-2.zip (GEN replicate 2)
m) EXP-21-BW5666_NIT-1.zip (NIT replicate 1)
n) EXP-22-BY2419_NIT-2.zip (NIT replicate 2)
o) EXP-21-BT2898_RIF-1.zip (RIF replicate 1)
p) EXP-21-BY1000_RIF-2.zip (RIF replicate 2)
q) EXP-21-BW5661_SPT-1.zip (SPT replicate 1)
r) EXP-21-BY1019_SPT-2.zip (SPT replicate 2)
s) EXP-21-BW5658_TET-1.zip (TET replicate 1)
t) EXP-22-BY2421_TET-1.zip (TET replicate 2)
<br>
<strong>2. 17h exposure to rifampicin (</strong><em><strong>E. coli</strong></em><strong>, </strong><em><strong>S. enterica</strong></em><strong>)</strong>
These experiments were performed to test the effect of long-term rifampicin exposure on <em>Escherichia coli</em> and <em>Salmonella enterica</em>.
a) EXP-21-BT2899.zip (<em>E. coli</em>)
b) EXP-21-BY1015.zip (<em>S. enterica</em>)
<br>
<strong>3. Growth in minimal medium (</strong><em><strong>E. coli</strong></em><strong>)</strong>
This experiment was performed to test how reducing the cellular growth rate (without antibiotics) affects the cell-to-cell growth heterogeneity.
a) EXP-22-BY2420.zip
<br>
<br>
<strong>Code</strong>
The 'codefolder' contains the ImAnalysis pipeline and the UNet used for image analysis. The scripts and parameter files to perform the image analysis are provided within each individual experiment folder. 
The 'Data_analysis' folder contains three directories: (i) 'Analysis_scripts', which contains the R scripts used for data analysis and figure generation; (ii) 'Raw_data', which contains the raw data underlying the figures in the paper; and (iii) 'Results', which is the output directory for the figures generated by the analysis scripts.
DOI: 10.7483/opendata.cms.c7h3.56o8
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH50_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.21518142
title: Immunoglobulin M and immunoglobulin G repertoire sequencing data of two donors first infected with SARS-CoV-2 then vaccinated with mRNA-1273

description: Immunoglobulin M (IgM) and immunoglobulin G (IgG) repertoire sequencing libraries from two donors who were first infected by index SARS-CoV-2, then vaccinated by the mRNA-1273 vaccine. We acquired longitudinal peripheral blood mononuclear cells (PBMCs) samples from each respective donor as follows: 11 or 14 days post-infection (acute timepoint), 32 or 37 days post-infection (convalescent timepoint), 160 or 169 days post-infection (pre-vax timepoint), and 9 or 7 days post-vaccination (post-vax timepoint). Three IgM libraries were generated from each donor for the Acute timepoint, as well as one IgG library per timepoint per donor for a total of 6 IgM and 6 IgG Rep-seq libraries.
DOI: 10.17044/scilifelab.21518142.v1
title: Immunoglobulin M and immunoglobulin G repertoire sequencing data of two donors first infected with SARS-CoV-2 then vaccinated with mRNA-1273

description: Immunoglobulin M (IgM) and immunoglobulin G (IgG) repertoire sequencing libraries from two donors who were first infected by index SARS-CoV-2, then vaccinated by the mRNA-1273 vaccine. We acquired longitudinal peripheral blood mononuclear cells (PBMCs) samples from each respective donor as follows: 11 or 14 days post-infection (acute timepoint), 32 or 37 days post-infection (convalescent timepoint), 160 or 169 days post-infection (pre-vax timepoint), and 9 or 7 days post-vaccination (post-vax timepoint). Three IgM libraries were generated from each donor for the Acute timepoint, as well as one IgG library per timepoint per donor for a total of 6 IgM and 6 IgG Rep-seq libraries.
DOI: 10.7483/opendata.cms.697l.fzbq
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH50_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.v8um.qwhg
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH75_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.zjrb.ykgo
title: /TprimeBToTH_TLep_Hbb_LH_MT2800_MH75_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.21407402.v1
title: Multi-site assessment of reproducibility in high-content live cell imaging data

description: This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data". 
<br>
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental chamber. The experiment was performed by 3 labs, 3 person in each lab, 3 independent experiments by each person, 3 technical replicates in each experiment, and two conditions (control and ROCK inhibition) for each technical repliates. 
<br>
The Data processing and analysis-2D.rar file contains the Matlab, CellProfiler, ImageJ, and R pipelines and scripts used in this study to process, quantify, and analyze the images. Detailed procedure could be found in the "Image processing and analysis procedures.txt" file within this .rar file.
<br>
The 3D Image data from Lab 1.zip and 3D Image data from Lab 2.zip contain the raw images and the quantified results of the 3D migration assay from Lab 1 and Lab 2, respectively. The experiment was performed with HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry embedded in 2.5mg/ml or 6mg/ml collagen I gels. The invasion of the cells from 3D spheroid was recorded with confocal microscopy 24 h after seeding. The experiment was performed by 2 labs, 3 independent experiments in each lab, 3 technical replicates in each experiment, and two conditions (2.5 mg/ml and 6 mg/ml of collagen I) for each technical repliates. 
<br>
The Meta data of the 3D experiment.zip contains the meta data of the 3D image data from Lab 1 (Radboudumc) and Lab 2 (Crick) as well as the software to read the meta data. After unzipping, ISAcreator program should be used to read the ISAfiles of Lab 1 or Lab 2.
<br>
The Fiji Plugins and parameters for 3D image data analysis.rar contains the Fiji plugins and also the parameters used during the 3D image data analysis.
<br>
The 3D Data Analysis Scripts.rar contains the R scripts used in this study to analyze the 3D data set, as well as the quantified results needed by the R scripts.
<br>
The Supplementary Materials 2-8.rar contains 2D experimental protocol (supplementary materials 2-4), 2D experimental survey (supplementary materials 3), and 3D experimental and image analysis protocols (supplementary materials 5-8) that are used in this study.
<br>
We encourage reuse using the same CC BY 4.0 License.
DOI: 10.7483/opendata.cms.cmds.dbl3
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.uoes.u3z1
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.21557247
title: Single cell sequencing data from: The complement receptor C3AR constitutes a novel therapeutic target in NPM1-mutated AML

description: This dataset contains single cell RNA sequencing data (fastq-files) from twelve NPM1-positive AML-samples. The single cell libraries were constructed from viably frozen cells from bone marrow (n=8) or peripheral blood (n=4) using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (10X genomics) and sequenced on a Novaseq 6000 or NextSeq 500.
DOI: 10.17044/scilifelab.21557247.v1
title: Single cell sequencing data from: The complement receptor C3AR constitutes a novel therapeutic target in NPM1-mutated AML

description: This dataset contains single cell RNA sequencing data (fastq-files) from twelve NPM1-positive AML-samples. The single cell libraries were constructed from viably frozen cells from bone marrow (n=8) or peripheral blood (n=4) using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (10X genomics) and sequenced on a Novaseq 6000 or NextSeq 500.
DOI: 10.7483/opendata.cms.s9vx.9dzt
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.15468/dl.6fkegk
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ischnomera xanthoderes (Mulsant, 1858)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 88 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071203-241126133413365/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.dohj.qqdn
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.2ivm.623s
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.ok11.ywkp
title: /TprimeBToTH_TLep_Hbb_LH_MT2900_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.15468/dl.y8k2bz
title: Occurrence Download

description: A dataset containing 106123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-6.39847 36.89241,-6.51316 36.70872,-6.16907 36.23603,-5.96835 36.13188,-5.58124 35.95799,-5.23715 36.13188,-5.0651 36.35159,-4.57764 36.45544,-4.11885 36.62822,-4.14752 37.24704,-4.76402 37.94,-5.19414 37.88344,-5.7963 37.72485,-6.31244 37.44081,-6.25509 37.00698,-6.39847 36.89241))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 106123 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071171-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.