SlideShare a Scribd company logo
May 10, 2024
Outline
● Brief introduction to the 4D Nucleome
● Finding data of interest in the portal
● Metadata and visualizing data on the portal
● Downloading Data Files
● Standardized bioinformatics pipelines
● Exploring Data
Pongubala and Murre, 2021
Imaging
B. Bintu lab, UCSD
Sequencing
Sequencing
Chromatin Conformation Capture
in situ Hi-C
Dilution Hi-C
DNase Hi-C
Micro-C, TCC
HiChip
PLAC-seq
ChIA-PET/Drop
Capture Hi-C
GAM
SPRITE
MARGI
4C-seq
DAMID-seq, TSA-seq, repli-seq,
CUT&RUN, ChIP-seq, ATAC-seq,
RNA-seq …
Additional Genomics Assays
Imaging
B. Bintu lab, UCSD
Multiplexed FISH
MERFISH, MINA,
OligoFISSEQ, ORCA,
seqFISH+,
OligoSTORM
DNA/RNA FISH,
Imunofluorescence,
SPT, OptoDroplet,
Electron Tomography
Additional Imaging Assays
LIVE PORTAL DEMO
https://data.4dnucleome.org
Useful Links
4DN Data portal - https://data.4dnucleome.org/
4DN Data Collections - https://data.4dnucleome.org/resources/data-collections
FISH Omics Format RTD - https://fish-omics-format.readthedocs.io/en/latest/
HiGlass tutorial video - https://www.youtube.com/watch?v=LEDaOa3NZtM
4DN-DCIC github - https://github.com/4dn-dcic/
Hi-C pipeline repo - https://github.com/4dn-dcic/docker-4dn-hic
4DN JupyterHub - https://data.4dnucleome.org/tools/jupyterhub
Data Portal Publication - https://pubmed.ncbi.nlm.nih.gov/35501320/
4DN Organizational Hub - https://www.4dnucleome.org/
Data portal paper in Nature Communications
Data portal
https://data.4dnucleome
.org/publications/ad9b5
72b-fe5e-4d9f-9ba3-7c6
2ff51ce9d/
Pubmed
https://pubmed.ncbi.nlm
.nih.gov/35501320/
Nature Communications
https://www.nature.com/
articles/s41467-022-296
97-4
4DN-DCIC
DBMI
Peter Park
Utku
Ozturk
Please reach out to us with questions,
comments or suggestions
support@4dnucleome.org

More Related Content

Similar to dkNET Webinar: The 4DN Data Portal - Data, Resources and Tools to Help Elucidate Nuclear Organization in Space and Time 05/10/2024

Forensics: Human Identity Testing in the Applied Genetics Group
Forensics: Human Identity Testing in the Applied Genetics GroupForensics: Human Identity Testing in the Applied Genetics Group
Forensics: Human Identity Testing in the Applied Genetics Group
Nathan Olson
 
Role of bioinformatics in life sciences research
Role of bioinformatics in life sciences researchRole of bioinformatics in life sciences research
Role of bioinformatics in life sciences research
Anshika Bansal
 
Data sharing and analysis
Data sharing and analysisData sharing and analysis
Data sharing and analysis
EURORDIS Rare Diseases Europe
 
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
Docker, Inc.
 
Submitted sequence (strains)
Submitted sequence (strains)Submitted sequence (strains)
Submitted sequence (strains)
Syeda Masoom Fatima
 
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseDevelopment of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
nist-spin
 
Giab for jax long read 190917
Giab for jax long read 190917Giab for jax long read 190917
Giab for jax long read 190917
GenomeInABottle
 
ImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial dataImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial data
Barry Smith
 
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysisTin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
GigaScience, BGI Hong Kong
 
Supporting high throughput high-biotechnologies in today’s research environme...
Supporting high throughput high-biotechnologies in today’s research environme...Supporting high throughput high-biotechnologies in today’s research environme...
Supporting high throughput high-biotechnologies in today’s research environme...
Ed Dodds
 
Howard University: Center for Computational Biology and Bioinformatics
Howard University: Center for Computational Biology and BioinformaticsHoward University: Center for Computational Biology and Bioinformatics
Howard University: Center for Computational Biology and Bioinformatics
karl.barnes
 
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
The Next, Next Generation of Sequencing - From Semiconductor to Single MoleculeThe Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
Justin Johnson
 
ngs.pptx
ngs.pptxngs.pptx
ngs.pptx
aaaa bbb
 

Similar to dkNET Webinar: The 4DN Data Portal - Data, Resources and Tools to Help Elucidate Nuclear Organization in Space and Time 05/10/2024 (13)

Forensics: Human Identity Testing in the Applied Genetics Group
Forensics: Human Identity Testing in the Applied Genetics GroupForensics: Human Identity Testing in the Applied Genetics Group
Forensics: Human Identity Testing in the Applied Genetics Group
 
Role of bioinformatics in life sciences research
Role of bioinformatics in life sciences researchRole of bioinformatics in life sciences research
Role of bioinformatics in life sciences research
 
Data sharing and analysis
Data sharing and analysisData sharing and analysis
Data sharing and analysis
 
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
Cool Genes: The Search for a Cure Using Genomics, Big Data, and Docker - Jame...
 
Submitted sequence (strains)
Submitted sequence (strains)Submitted sequence (strains)
Submitted sequence (strains)
 
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseDevelopment of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Database
 
Giab for jax long read 190917
Giab for jax long read 190917Giab for jax long read 190917
Giab for jax long read 190917
 
ImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial dataImmPort strategies to enhance discoverability of clinical trial data
ImmPort strategies to enhance discoverability of clinical trial data
 
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysisTin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee: GDSAP- A Galaxy-based platform for large-scale genomics analysis
 
Supporting high throughput high-biotechnologies in today’s research environme...
Supporting high throughput high-biotechnologies in today’s research environme...Supporting high throughput high-biotechnologies in today’s research environme...
Supporting high throughput high-biotechnologies in today’s research environme...
 
Howard University: Center for Computational Biology and Bioinformatics
Howard University: Center for Computational Biology and BioinformaticsHoward University: Center for Computational Biology and Bioinformatics
Howard University: Center for Computational Biology and Bioinformatics
 
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
The Next, Next Generation of Sequencing - From Semiconductor to Single MoleculeThe Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
 
ngs.pptx
ngs.pptxngs.pptx
ngs.pptx
 

More from dkNET

dkNET Office Hours: NIH Data Management and Sharing Mandate 05/03/2024
dkNET Office Hours: NIH Data Management and Sharing Mandate  05/03/2024dkNET Office Hours: NIH Data Management and Sharing Mandate  05/03/2024
dkNET Office Hours: NIH Data Management and Sharing Mandate 05/03/2024
dkNET
 
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
dkNET
 
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
dkNET
 
dkNET Webinar: Tabula Sapiens 03/22/2024
dkNET Webinar: Tabula Sapiens 03/22/2024dkNET Webinar: Tabula Sapiens 03/22/2024
dkNET Webinar: Tabula Sapiens 03/22/2024
dkNET
 
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
dkNET
 
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
dkNET
 
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET
 
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
dkNET
 
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
dkNET
 
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET
 
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
dkNET
 
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
dkNET
 
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
dkNET
 
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET
 
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
dkNET
 
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
dkNET
 
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
dkNET
 
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
dkNET
 
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
dkNET
 
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
dkNET
 

More from dkNET (20)

dkNET Office Hours: NIH Data Management and Sharing Mandate 05/03/2024
dkNET Office Hours: NIH Data Management and Sharing Mandate  05/03/2024dkNET Office Hours: NIH Data Management and Sharing Mandate  05/03/2024
dkNET Office Hours: NIH Data Management and Sharing Mandate 05/03/2024
 
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
dkNET Webinar "Texera: A Scalable Cloud Computing Platform for Sharing Data a...
 
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
dkNET Webinar: Unlocking the Power of FAIR Data Sharing with ImmPort 04/12/2024
 
dkNET Webinar: Tabula Sapiens 03/22/2024
dkNET Webinar: Tabula Sapiens 03/22/2024dkNET Webinar: Tabula Sapiens 03/22/2024
dkNET Webinar: Tabula Sapiens 03/22/2024
 
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
dkNET Webinar "The Multi-Omic Response to Exercise Training Across Rat Tissue...
 
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...
 
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
 
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
dkNET Webinar: A Single Cell Atlas of Human and Mouse White Adipose Tissue 11...
 
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
dkNET Webinar "The National Sleep Research Resource (NSRR) - Opportunities fo...
 
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
 
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch 06/02/2023
 
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
dkNET Webinar: Leveraging Computational Strategies to Identify Type 1 Diabete...
 
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
dkNET Webinar: Estimating Relative Beta-Cell Function During Continuous Gluco...
 
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023: New NIH Data Management and Sha...
 
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
dkNET Webinar: Postpartum Glucose Screening Among Homeless Women with Gestati...
 
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
dkNET Webinar: Choosing Sample Sizes for Multilevel and Longitudinal Studies ...
 
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
dkNET Webinar: : FAIR Data Curation of Antibody/B-cell and T-cell Receptor Se...
 
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
dkNET Office Hours - "Are You Ready for 2023? New NIH Data Management and Sha...
 
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
dkNET Webinar "The Mission and Progress of the(sugar)science: Helping Scienti...
 
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
dkNET Webinar: Discovering and Evaluating Antibodies, Cell Lines, Software To...
 

Recently uploaded

Embracing Deep Variability For Reproducibility and Replicability
Embracing Deep Variability For Reproducibility and ReplicabilityEmbracing Deep Variability For Reproducibility and Replicability
Embracing Deep Variability For Reproducibility and Replicability
University of Rennes, INSA Rennes, Inria/IRISA, CNRS
 
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Sérgio Sacani
 
LEARNING TO LIVE WITH LAWS OF MOTION .pptx
LEARNING TO LIVE WITH LAWS OF MOTION .pptxLEARNING TO LIVE WITH LAWS OF MOTION .pptx
LEARNING TO LIVE WITH LAWS OF MOTION .pptx
yourprojectpartner05
 
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
frank0071
 
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Sérgio Sacani
 
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Creative-Biolabs
 
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDSJAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
Sérgio Sacani
 
Clinical periodontology and implant dentistry 2003.pdf
Clinical periodontology and implant dentistry 2003.pdfClinical periodontology and implant dentistry 2003.pdf
Clinical periodontology and implant dentistry 2003.pdf
RAYMUNDONAVARROCORON
 
Methods of grain storage Structures in India.pdf
Methods of grain storage Structures in India.pdfMethods of grain storage Structures in India.pdf
Methods of grain storage Structures in India.pdf
PirithiRaju
 
11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf
PirithiRaju
 
Reaching the age of Adolescence- Class 8
Reaching the age of Adolescence- Class 8Reaching the age of Adolescence- Class 8
Reaching the age of Adolescence- Class 8
abhinayakamasamudram
 
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdfHolsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
frank0071
 
Microbiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdfMicrobiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
sammy700571
 
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
BIRDS  DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxBIRDS  DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
goluk9330
 
Lattice Defects in ionic solid compound.pptx
Lattice Defects in ionic solid compound.pptxLattice Defects in ionic solid compound.pptx
Lattice Defects in ionic solid compound.pptx
DrRajeshDas
 
cathode ray oscilloscope and its applications
cathode ray oscilloscope and its applicationscathode ray oscilloscope and its applications
cathode ray oscilloscope and its applications
sandertein
 
Post translation modification by Suyash Garg
Post translation modification by Suyash GargPost translation modification by Suyash Garg
Post translation modification by Suyash Garg
suyashempire
 
Farming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptxFarming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptx
Frédéric Baudron
 
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
HUMAN EYE By-R.M Class 10 phy best digital notes.pdfHUMAN EYE By-R.M Class 10 phy best digital notes.pdf
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
Ritik83251
 
23PH301 - Optics - Unit 2 - Interference
23PH301 - Optics - Unit 2 - Interference23PH301 - Optics - Unit 2 - Interference
23PH301 - Optics - Unit 2 - Interference
RDhivya6
 

Recently uploaded (20)

Embracing Deep Variability For Reproducibility and Replicability
Embracing Deep Variability For Reproducibility and ReplicabilityEmbracing Deep Variability For Reproducibility and Replicability
Embracing Deep Variability For Reproducibility and Replicability
 
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
 
LEARNING TO LIVE WITH LAWS OF MOTION .pptx
LEARNING TO LIVE WITH LAWS OF MOTION .pptxLEARNING TO LIVE WITH LAWS OF MOTION .pptx
LEARNING TO LIVE WITH LAWS OF MOTION .pptx
 
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
 
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
 
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
 
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDSJAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
 
Clinical periodontology and implant dentistry 2003.pdf
Clinical periodontology and implant dentistry 2003.pdfClinical periodontology and implant dentistry 2003.pdf
Clinical periodontology and implant dentistry 2003.pdf
 
Methods of grain storage Structures in India.pdf
Methods of grain storage Structures in India.pdfMethods of grain storage Structures in India.pdf
Methods of grain storage Structures in India.pdf
 
11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf
 
Reaching the age of Adolescence- Class 8
Reaching the age of Adolescence- Class 8Reaching the age of Adolescence- Class 8
Reaching the age of Adolescence- Class 8
 
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdfHolsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
 
Microbiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdfMicrobiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
 
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
BIRDS  DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxBIRDS  DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
 
Lattice Defects in ionic solid compound.pptx
Lattice Defects in ionic solid compound.pptxLattice Defects in ionic solid compound.pptx
Lattice Defects in ionic solid compound.pptx
 
cathode ray oscilloscope and its applications
cathode ray oscilloscope and its applicationscathode ray oscilloscope and its applications
cathode ray oscilloscope and its applications
 
Post translation modification by Suyash Garg
Post translation modification by Suyash GargPost translation modification by Suyash Garg
Post translation modification by Suyash Garg
 
Farming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptxFarming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptx
 
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
HUMAN EYE By-R.M Class 10 phy best digital notes.pdfHUMAN EYE By-R.M Class 10 phy best digital notes.pdf
HUMAN EYE By-R.M Class 10 phy best digital notes.pdf
 
23PH301 - Optics - Unit 2 - Interference
23PH301 - Optics - Unit 2 - Interference23PH301 - Optics - Unit 2 - Interference
23PH301 - Optics - Unit 2 - Interference
 

dkNET Webinar: The 4DN Data Portal - Data, Resources and Tools to Help Elucidate Nuclear Organization in Space and Time 05/10/2024

  • 2. Outline ● Brief introduction to the 4D Nucleome ● Finding data of interest in the portal ● Metadata and visualizing data on the portal ● Downloading Data Files ● Standardized bioinformatics pipelines ● Exploring Data
  • 3.
  • 5. Imaging B. Bintu lab, UCSD Sequencing
  • 6. Sequencing Chromatin Conformation Capture in situ Hi-C Dilution Hi-C DNase Hi-C Micro-C, TCC HiChip PLAC-seq ChIA-PET/Drop Capture Hi-C GAM SPRITE MARGI 4C-seq DAMID-seq, TSA-seq, repli-seq, CUT&RUN, ChIP-seq, ATAC-seq, RNA-seq … Additional Genomics Assays
  • 7. Imaging B. Bintu lab, UCSD Multiplexed FISH MERFISH, MINA, OligoFISSEQ, ORCA, seqFISH+, OligoSTORM DNA/RNA FISH, Imunofluorescence, SPT, OptoDroplet, Electron Tomography Additional Imaging Assays
  • 9. Useful Links 4DN Data portal - https://data.4dnucleome.org/ 4DN Data Collections - https://data.4dnucleome.org/resources/data-collections FISH Omics Format RTD - https://fish-omics-format.readthedocs.io/en/latest/ HiGlass tutorial video - https://www.youtube.com/watch?v=LEDaOa3NZtM 4DN-DCIC github - https://github.com/4dn-dcic/ Hi-C pipeline repo - https://github.com/4dn-dcic/docker-4dn-hic 4DN JupyterHub - https://data.4dnucleome.org/tools/jupyterhub Data Portal Publication - https://pubmed.ncbi.nlm.nih.gov/35501320/ 4DN Organizational Hub - https://www.4dnucleome.org/
  • 10. Data portal paper in Nature Communications Data portal https://data.4dnucleome .org/publications/ad9b5 72b-fe5e-4d9f-9ba3-7c6 2ff51ce9d/ Pubmed https://pubmed.ncbi.nlm .nih.gov/35501320/ Nature Communications https://www.nature.com/ articles/s41467-022-296 97-4
  • 12. Please reach out to us with questions, comments or suggestions support@4dnucleome.org