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text: not provided

text: house mouse

text: Protocols: Tumor-explant-derived cell lines were collected from GEM model primary pancreatic tumors using mechanical and chemical dissociation with 2mg/mL Dispase and 2mg/mL Collagenase IV. After 1h incubation at 37C 5%CO2, cells were centrifuged at 200 g for 5 minutes. Single cell suspensions were plated in a sufficient amount of medium. Short-term cultures were obtained; epithelial (EPI) and mesenchymal (MS) populations from the same tumor were derived with ganciclovir (GCV) treatment (5uM) in vitro. After stabilization of EPI and MS populations, cells were collected with trypsinization, centrifuged at 200g for 5 minutes, resuspended in Bambanker and stored in liquid nitrogen for downstream processing Nucleic acids were directly processed on intact cells following standard Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics) using Chromium platform (10x Genomics). Target cell recovery was 5'000. Libraries were prepared using Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics). Library quality was assessed using TapeStation (Agilent Technologies). Libraries were sequenced on NovaSeq 6000 platform (Illumina) aiming at 50'000 clusters/cell.

text: pancreatic cancer

characteristic: disease

text: not provided

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: pancreas

characteristic: organism part

text: epithelial

characteristic: phenotype

text: tumor

characteristic: sampling site

text: Mus musculus


characteristic: ENA first public

text: Center for Omics Sciences IRCCS Ospedale San Raffaele

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: tumor-derived primary cell line

text: not provided

text: house mouse

text: pancreatic cancer

text: not provided

text: not applicable

text: Mus musculus

text: Mus musculus

text: pancreas

text: mesenchymal

text: tumor

text: Mus musculus

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: tumor-derived primary cell line

text: not provided

characteristic: collection date

text: house mouse

characteristic: common name

text: Protocols: Tumor-explant-derived cell lines were collected from GEM model primary pancreatic tumors using mechanical and chemical dissociation with 2mg/mL Dispase and 2mg/mL Collagenase IV. After 1h incubation at 37C 5%CO2, cells were centrifuged at 200 g for 5 minutes. Single cell suspensions were plated in a sufficient amount of medium. Short-term cultures were obtained; epithelial (EPI) and mesenchymal (MS) populations from the same tumor were derived with ganciclovir (GCV) treatment (5uM) in vitro. After stabilization of EPI and MS populations, cells were collected with trypsinization, centrifuged at 200g for 5 minutes, resuspended in Bambanker and stored in liquid nitrogen for downstream processing Nucleic acids were directly processed on permeabilized nuclei following the “Nuclei Isolation for Single Cell ATAC Sequencing” protocol CG000169, Rev D (10X Genomics). Specifically, we prepared the nuclei suspension in order to get 5’000 nuclei as target nuclei recovery. Single-cell GET-seq was performed on Chromium platform (10x Genomics) following “Chromium Single Cell ATAC Reagent Kits” user manual version CG000168 Rev C. For GET-seq protocol, Tn5 and TnH were used in substitution of the 10X ATAC enzyme (10X Genomics) in the transposition mix assembly step. When a sequential Tn5 to TnH reaction was performed, a transposition mix containing 1.5 uL of Tn5 was incubated 30 min at 37 °C, then 1.5 uL of TnH was added and the reaction was continued for a total of 1 h incubation.

text: pancreatic cancer

text: not provided

text: not applicable

text: Mus musculus

text: Mus musculus

text: pancreas

text: epithelial

text: tumor

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: tumor-derived primary cell line

text: not provided

text: house mouse

characteristic: description

text: pancreatic cancer

text: not provided

text: not applicable

text: Mus musculus

text: Mus musculus

text: pancreas

text: mesenchymal

text: tumor

text: Mus musculus


name: SAMIN0003735-Transcriptomic analysis of mice lungs infected with H37Rv wildtype MTB

text: Rahul Pal and Amit Kumar Pandey THSTI

text: public

tag: Namespace:Rahul Pal and Amit Kumar Pandey THSTI

text: IBDC

characteristic: broker name

text: Rahul Pal

text: house mouse

text: India

characteristic: geographic location (country and/or sea)

text: THSTI, Faridabad, India

characteristic: geographic location (region and locality)

text: Mus musculus

characteristic: host scientific name

text: 8 weeks

text: Tuberculosis

text: Female

text: Mice infected with wild type M. tuberculosis

text: Mouse

text: Mus musculus

text: Mus musculus

characteristic: strain

text: Lungs


name: SAMIN0003736-Transcriptomic analysis of mice lungs infected with Rv0495c mutant of M. tuberculosis

characteristic: ENA first public

text: Rahul Pal and Amit Kumar Pandey THSTI

text: public

text: IBDC

text: Rahul Pal

text: house mouse

text: India

text: THSTI, Faridabad, India

text: Mus musculus

text: 8 weeks

text: Tuberculosis

text: Female

text: Mice infected with Rv0495c mutant of M. tuberculosis

text: Mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Lungs


text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Blue mussels

text: Norway

text: Escherichia coli

text: Escherichia coli


text: NORWEGIAN VETERINARY INSTITUTE

text: public

characteristic: SRA accession

text: Ocean quahog

text: Norway

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: NORWEGIAN VETERINARY INSTITUTE

text: public

characteristic: Submitter Id

characteristic: collection date

text: Great scallops

text: Norway

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: Flat oysters

text: Norway

text: Escherichia coli

text: Escherichia coli


characteristic: External Id

text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: Great scallpos

text: Norway

text: Escherichia coli

text: Escherichia coli


E-MTAB-13364:Sample 1

characteristic: INSDC center name

text: public

text: E-MTAB-13364:Sample 1

tag: Namespace:Sun Yat-sun University Zhongshan Ophathlamic Center

text: 4 to 15

unit: year

characteristic: age

text: ArrayExpress

text: not collected

text: crab-eating macaque

characteristic: common name

text: Protocols: Total 8 monkeys (4-15 years old, males only, Macaca fascicularis) were used in the current project. All procedures complied with the NIH Guide for the Care and Use of Laboratory Animals approved by Sun Yat-sen University. Following 2 weeks of adaptive housing in the institutional animal facility, animals were anesthetized with a lethal dose of sodium pentobarbital. Animals were transcardially perfused with 2 liters of artificial cerebrospinal fluid (ACSF, in mM: 125 NaCl, 25 NaHCO3, 1 NaH2PO4, 2 KCl, 25 D-Glucose, 2 CaCl2, 1 MgCl2, 5 sodium l-ascorbate, 3 sodium pyruvate, 0.01 taurine, 2 thiourea, 1 kynurenic acid, 0.1 DL-AP5, and 1x10-3 tetrodotoxin). The flow of perfusion fluid was adjusted so that the perfusion finished within approximately 40 minutes. The brain was removed from the skull immediately and a block of tissue containing the LIP was cut off. The position of LIP referred to the atlas of the rhesus monkey brain (Saleem and Logothetis, 2012). The tissue block was kept in the ACSF and snap frozen. The brain was removed from the skull immediately and a block of tissue containing the LIP was cut off. The single-nuclei suspensions were prepared following previously described methods (Krishnaswami et al. 2016), with some modifications. Briefly, the frozen brain tissues were lysed gently in a glass dounce homogenizer with 2 ml ice-cold Lysis solution, consisting of 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10mM Tris buffer pH 8.0, 1mM DTT, 40 U/µL100x protease inhibitor, RNAse Inhibitor, and 0.1% Triton X-100. The lysate was kept on ice for 5 minutes and then filtered through a 40 μm filter (BD Falcon, 352350) to eliminate cell clumps. The nuclei pellets were collected by centrifuging the lysate at 500 g for 5 minutes and discarding the supernatant. The nuclei were then purified with density gradient centrifugation buffer solutions (25% and 29% iodixanol solution in 250 mM sucrose, 25 mM KCl, 5mM MgCl2, and 10 mM Tris buffer, pH 8.0) and centrifuged for 30 minutes at 13500g. The nuclei pellets were washed and stored at a resuspension buffer consisting of 1% UltraPure BSA (Sigma, B2064), 0.2 U/µL Rnase Inhibitor, in Rnase-free PBS (Gibco, C1001050BT). Nuclei suspensions with a viability of > 90% were used for snRNA-seq library and sequencing. Following the protocols provided by 10X Genomics Chromium platform.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of 8 individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Macaca fascicularis

text: Macaca fascicularis

text: brain

characteristic: organism part

text: lateral intraparietal cortex

characteristic: sampling site

text: Macaca fascicularis

text: male

characteristic: sex

text: Sample 1


characteristic: ENA first public

text: Eotvos Lorand University

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Eotvos Lorand University

characteristic: description

text: Williamsburg

text: Virginia

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Williamsburg Plant

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Eotvos Lorand University

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Norfolk

text: Virginia

text: USA

text: metagenome

text: Virginia Initiative Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Eotvos Lorand University

characteristic: INSDC last update

text: public

text: Suffolk

text: Virginia

text: USA

text: metagenome

text: Nansemond Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

characteristic: INSDC status

characteristic: description

text: Virginia Beach

text: Virginia

text: USA

text: metagenome

text: Atlantic Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Virginia Beach

text: Virginia

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Chez-Liz Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: York River/Gloucester

text: Virginia

text: USA

text: metagenome

text: York River Plant

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Newport News

text: Virginia

text: USA

text: metagenome

text: James River Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Eotvos Lorand University

text: public

text: Newport News/Hampton

text: Virginia

text: USA

text: metagenome

text: Boat Harbor Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

tag: Namespace:Technical University of Denmark

text: Norfolk

text: Virginia

text: USA

text: metagenome

text: Army Base Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Virginia Beach

text: Virginia

text: USA

text: metagenome

text: Atlantic Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Seattle

text: Washington

text: USA

text: metagenome

text: WestPoint

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Renton

text: Washington

text: USA

text: metagenome

text: Renton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Woodinville

text: Washington

text: USA

text: metagenome

text: Brightwater

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Dayton

text: Ohio

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Dayton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Marysville

text: Ohio

text: USA

text: metagenome

text: Marysville

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Troy

text: Ohio

text: USA

text: metagenome

text: Troy

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Eotvos Lorand University

text: public

text: Jackson Pike

text: Ohio

text: USA

text: metagenome

text: Jackson Pike WWP

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Eotvos Lorand University

characteristic: INSDC center name

text: public

text: South Milwaukee

text: Wisconsin

text: USA

text: metagenome

text: South Milwaukee

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Brookfield

text: Wisconsin

text: USA

text: metagenome

text: Brookfield

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

characteristic: collection date

text: Oak Creek

text: Wisconsin

text: USA

text: metagenome

text: Oak Creek South shore WRF

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Eotvos Lorand University

characteristic: INSDC last update

text: public

text: Milwaukee Jones Island

text: Wisconsin

text: USA

text: metagenome

text: Milwaukee Jones Island WRF

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

characteristic: INSDC status

characteristic: description

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: South River

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Atlanta

text: Georgia

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Utoy

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: RL Sutton

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

text: Falkenburg

text: Florida

text: USA

text: metagenome

text: Falkenburg

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Eotvos Lorand University

text: public

text: Avila

text: Florida

text: USA

text: metagenome

text: Avila

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Eotvos Lorand University

characteristic: INSDC center name

text: public

text: Gretna Green

text: Florida

text: USA

text: metagenome

text: Gretna Green

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Eotvos Lorand University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Eden

text: Florida

text: USA

text: metagenome

text: Eden

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Eden

text: Florida

text: USA

text: metagenome

text: Eden

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Heather Field

text: Florida

text: USA

text: metagenome

text: Heather Field

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Tacoma

text: Washington

text: USA

text: metagenome

text: Tacoma

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Woodinville

text: Washington

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Brightwater

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Sumner

text: Washington

text: USA

text: metagenome

text: Sumner

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Renton

text: Washington

text: USA

text: metagenome

text: Renton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Edmonds

text: Washington

text: USA

text: metagenome

text: Edmonds

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: Seattle

text: Washington

text: USA

text: metagenome

text: WestPoint

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Charleston

text: Illinois

text: USA

text: metagenome

text: Charleston

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Troy

text: Illinois

text: USA

text: metagenome

text: Troy

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Gillespie

text: Illinois

text: USA

text: metagenome

text: Gillespie

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Benld

text: Illinois

text: USA

text: metagenome

text: Benld

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Atlanta

text: Georgia

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: South River

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: RM Clayton

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: Utoy

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: RL Sutton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: not provided

text: Atlanta

text: Georgia

text: USA

text: metagenome

text: RL Sutton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Christiansburg

text: Virginia

text: USA

text: metagenome

text: Christiansburg

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Blacksburg

text: Virginia

text: USA

text: metagenome

text: Blacksburg

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Dayton

text: Ohio

text: USA

text: metagenome

text: Dayton

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Marion

text: Ohio

text: USA

text: metagenome

text: Marion

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Jackson Pike

text: Ohio

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Jackson Pike WWP

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Troy

text: Ohio

text: USA

text: metagenome

text: Troy

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Marysville

text: Ohio

text: USA

text: metagenome

text: Marysville

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Virginia Beach

text: Virginia

text: USA

text: metagenome

text: Chez-Liz Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: Virginia Beach

text: Virginia

text: USA

text: metagenome

text: Atlantic Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Norfolk

text: Virginia

text: USA

text: metagenome

text: Virginia Initiative Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Norfolk

text: Virginia

text: USA

text: metagenome

text: Army Base Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Newport News

text: Virginia

text: USA

text: metagenome

text: James River Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Newport News/Hampton

text: Virginia

text: USA

text: metagenome

text: Boat Harbor Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Williamsburg

text: Virginia

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Williamsburg Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: York River/Gloucester

text: Virginia

text: USA

text: metagenome

text: York River Plant

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Suffolk

text: Virginia

text: USA

text: metagenome

text: Nansemond Plant

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Chapel Hill

text: North Carolina

text: USA

text: metagenome

text: Michael+Emanuele

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: Chapel Hill

text: North Carolina

text: USA

text: metagenome

text: Kat+Emanuele

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Milwaukee Jones Island

text: Wisconsin

text: USA

text: metagenome

text: Milwaukee Jones Island WRF

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: South Milwaukee

text: Wisconsin

text: USA

text: metagenome

text: South Milwaukee

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Brookfield

text: Wisconsin

text: USA

text: metagenome

text: Brookfield

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: INSDC status

characteristic: description

text: Fond du Lac

text: Wisconsin

text: USA

text: metagenome

text: Fond du Lac

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Falkenburg

text: Florida

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

text: Falkenburg

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Avila

text: Florida

text: USA

text: metagenome

text: Avila

characteristic: name of the sampling site

text: PCR free

characteristic: nucleic acid amplification

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

text: Gretna Green

text: Florida

text: USA

text: metagenome

text: Gretna Green

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

characteristic: nucleic acid extraction

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Eden

text: Florida

text: USA

text: metagenome

text: Eden

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: Heather Field

text: Florida

text: USA

text: metagenome

text: Heather Field

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Cincinnati

text: Ohio

text: USA

text: metagenome

text: Mill Creek

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: Technical University of Denmark

text: public

characteristic: collection date

text: Cincinnati

text: Ohio

text: USA

text: metagenome

text: Muddy Creek

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: title


characteristic: ENA first public

text: Technical University of Denmark

characteristic: INSDC last update

text: public

text: Cincinnati

text: Ohio

text: USA

text: metagenome

text: Sycamore Creek

text: PCR free

text: QIAamp Fast DNA Stool Mini Kit

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant


text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-13524:Irx3_ChIP-seq_gWAT_Day1_Input

tag: Namespace:University of Bergen

text: 6 to 10

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

characteristic: common name

text: Protocols: Mouse inguinal and gonadal white adipose tissues where excised from 6-10 weeks old C57BL/6NJ (B6N) mice fed ad libitum with SDS maintenance chow (RM3, 3.6 kcal/g). Primary preadipocytes were isolated from the WAT depots by by collagenase digestion and centrifugation to separate floating adipocytes from the SVF pellet. The SVF was resuspended in DMEM GlutaMax culture medium supplemented with 10% FBS and 1% PEST. The cell suspension was filtered through a 40 um mesh and pooled cells from 6-12 mice were seeded on a 10 cm dish at a density of 100.000 cells/mL. Cells were grown to confluence, and induced to differentiate 2 days post confluency by addition of 0.5 mM IBMX, 1 uM Dex, 5 ug/mL human Insulin to the growth media. On days -1 and 1 of differentiation, cells were fixated by addition of 1/10 volume of freshly prepared formaldehyde solution (11% formaldehyde, 0.1 M NaCl, 1mM EDTA pH 8.0 and 50 mM HEPES pH 7.9) to the culture media. After 15 minutes, the fixation reaction was stopped by addition of 1/20 volume of 2.5 M glycine. The cells were thereafter kept on ice and washed twice with 0.5% Igepal in PBS. In the second wash, 1mM PMSF was added. Pellets were snap-frozen in liquid nitrogen and stored at -80oC until shipment on dry ice to Active Motif for ChIP-sequencing Nucleic acid extraction was performed by Active Motif by in-house protocols based on public protocols:Park, P.J., 2009. ChIP–seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 10: 669–80.Pepke, S., Wold, B., Mortazavi, A., 2009. Computation for chip-seq and rna-seq studies. Nature Methods 6(11 Suppl): S22-32.Furey, T.S., 2012. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nature Reviews Genetics 13(12): 840–52. Nucleic acid library construction was performed by Active Motif by in-house protocols based on public protocols:Park, P.J., 2009. ChIP–seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 10: 669–80.Pepke, S., Wold, B., Mortazavi, A., 2009. Computation for chip-seq and rna-seq studies. Nature Methods 6(11 Suppl): S22-32.Furey, T.S., 2012. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nature Reviews Genetics 13(12): 840–52.

characteristic: description

text: Day 1 of adipogenic differentiation

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: adipose tissue of abdominal region

characteristic: organism part

text: a

characteristic: replicate

text: Mus musculus

text: C57BL/6NJ (B6N)

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

text: Day 1 of adipogenic differentiation

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: adipose tissue of abdominal region

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)


characteristic: ENA first public

text: University of Bergen

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_Day_-1_input

characteristic: Submitter Id

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: preadipocyte

text: not collected

characteristic: collection date

text: house mouse

text: Day -1 of adipogenic differentiation

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: subcutaneous adipose tissue

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)

characteristic: title


text: University of Bergen

text: public

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_day_-1_parallel_a

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: Day -1 of adipogenic differentiation

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: subcutaneous adipose tissue

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Bergen

text: public

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_Day_-1_parallel_b

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

text: Day -1 of adipogenic differentiation

text: wild type genotype

text: not collected

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: subcutaneous adipose tissue

characteristic: organism part

text: b

characteristic: replicate

text: Mus musculus

text: C57BL/6NJ (B6N)

characteristic: strain


characteristic: ENA first public

text: University of Bergen

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_Day_1_Input

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

text: Day 1 of adipogenic differentiation

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: subcutaneous adipose tissue

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)


text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_Day_1_parallel_a

characteristic: Submitter Id

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: preadipocyte

text: not collected

characteristic: collection date

text: house mouse

text: Day 1 of adipogenic differentiation

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: subcutaneous adipose tissue

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Bergen

text: public

text: E-MTAB-13524:Irx3_ChIP_seq_iWAT_Day_1_parallel_b

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: preadipocyte

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: Day 1 of adipogenic differentiation

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: subcutaneous adipose tissue

text: a

text: Mus musculus

text: C57BL/6NJ (B6N)


characteristic: ENA first public

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277252

tag: Namespace:Hospital General Universitario Gregorio Maranon

text: Spain

text: not applicable

characteristic: host health state

text: Human

characteristic: host scientific name

characteristic: isolate

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Hospital General Universitario Gregorio Maranon

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277253

text: Spain

characteristic: geographic location (country and/or sea)

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277254

characteristic: Submitter Id

characteristic: collection date

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277255

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277256

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277257

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277258

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:315-277259

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277260

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277262

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277263

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277264

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277265

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277266

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277267

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277268

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277269

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Hospital General Universitario Gregorio Maranon

text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:316-277270

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277271

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277272

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277273

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277274

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277275

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277276

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277277

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277278

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277279

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277280

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:317-277281

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277283

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277284

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277285

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277286

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Hospital General Universitario Gregorio Maranon

text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277288

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277289

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277290

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277291

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277292

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277293

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277294

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:318-277295

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277296

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277297

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277298

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277300

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277301

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277302

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277303

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277304

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Hospital General Universitario Gregorio Maranon

text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277305

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277307

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:319-277308

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:320-277309

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:320-277310

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:320-277311

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:320-277312

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-12:38:34:320-277313

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:619-2230

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:620-2231

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:620-2232

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:620-2233

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:620-2234

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:620-2235

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2236

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis variant caprae


text: Hospital General Universitario Gregorio Maranon

text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2237

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2238

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2239

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2240

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:621-2241

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2242

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2243

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2244

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2245

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2246

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2247

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:622-2248

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2249

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2250

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2251

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2252

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Hospital General Universitario Gregorio Maranon

text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2253

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: public

text: ena-SAMPLE-TAB-16-01-2024-14:24:57:623-2254

text: Spain

text: not applicable

text: Human

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


E-MTAB-13757:Sample 1

text: public

text: E-MTAB-13757:Sample 1

tag: Namespace:Instituto de Medicina Molecular João Lobo Antunes

text: ArrayExpress

characteristic: broker name

text: iPSC derived cell line

text: cardiac muscle cell

text: not collected

text: human

characteristic: common name

text: Protocols: All iPSCs were seeded on plates coated with Matrigel™ (Corning) and cultured in mTeSR™1 Medium (Stem Cell Technologies). Medium was changed daily. Cells were split every 3-4 days (when the colonies covered approximately 85% of the surface area of the culture dish) using PBS 0.5mM EDTA dissociation buffer. Before each differentiation process, iPSCs were thawed and maintained in culture for 2-3 passages. Before seeding, cells were incubated with ROCKi (Y-27632, 10μM, Stem Cell Technologies) for 1 h at 37ºC and then treated with Accutase (Sigma) for 7 min at 37ºC for dissociation. Microwell plates (AggreWell™800, Stem Cell Technologies) were used to generate aggregates. Cells were plated at a density of 0.9 x 106cells/well (3,000 cells/microwell) in 1.5 mL/well of mTeSR™1 supplemented with 10μM ROCKi. After 24 hours, the full volume of the medium was replaced and aggregates were maintained in mTeSR™1 without ROCKi for 48h. From this time point on (day 0 of differentiation), RPMI 1640 (Thermo Fisher Scientific) was used as the basal medium. During the first 7 days, cells were cultured in RPMI supplemented with 2%(v/v) B-27 minus insulin (Thermo Fisher Scientific). After day 7, cells were cultured in RPMI supplemented with 2%(v/v) B-27 (Thermo Fisher Scientific) until the end of differentiation. At day 0 of differentiation, the Wnt signaling pathway was activated using the GSK3 inhibitor CHIR99021 (Stemgent) at a final concentration of 11 µM. After 24 hours (day 1), full-volume medium replacement with RPMI + B27 minus insulin was performed. On day 3, half of the medium in each well was replaced and cells were supplemented with Wnt inhibitor IWP-4 (Stemgent) at a final concentration of 5 µM for two days. On day 5, the total volume of medium was changed. On day 7, the aggregates were flushed from the AggreWell™800 plate with RPMI + B27 and transferred to ultra-low attachment 6-well plates (Costar, Corning). On day 10, the full volume of medium was replaced. On day 13, aggregates were dissociated using 0,25% Trypsin-EDTA (Gibco) for 7 min at 37ºC. After dissociation, cells were washed with 2% fetal bovine serum (FBS) and 2mM EDTA in phosphate buffered saline (PBS, 0.1M), and incubated with VCAM1 antibody (BioLegend, 1:50) diluted in PBS/2% FBS for 15 min at 4ºC. Then, cells were washed and suspended in PBS/2% FBS for FACS sorting (BD FACSAria™ III Cell Sorter) using a 100μm nozzle at 4ºC. Purified VCAM1 positive cells were plated on wells coated with Matrigel, at a seeding density between 20,000 – 40,000 cells/cm2. For the remaining time in culture, two-thirds of the total volume of RPMI + B27 was replaced every 2–3 days. RNA was extracted using NZYol (NZYTech®) and digested with DNase I (Roche®). At least 1µg of total RNA was obtained from each culture of iPSC-CMs at day 30 of differentiation. After purification with poly-T oligo-attached magnetic beads, libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit.

characteristic: description

text: embryo

characteristic: developmental stage

text: wild type genotype

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

characteristic: replicate

text: day 30 of differentiation

characteristic: sampling time point

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1


E-MTAB-13757:Sample 2

characteristic: ENA first public

text: Instituto de Medicina Molecular João Lobo Antunes

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: E-MTAB-13757:Sample 2

text: ArrayExpress

text: iPSC derived cell line

text: cardiac muscle cell

text: not collected

text: human

text: embryo

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: day 30 of differentiation

text: Homo sapiens

text: male

text: Sample 2


E-MTAB-13757:Sample 3

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13757:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: iPSC derived cell line

text: cardiac muscle cell

text: not collected

text: human

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: day 30 of differentiation

text: Homo sapiens

text: female

text: Sample 3


characteristic: ENA-CHECKLIST

characteristic: External Id

text: W-cq

text: public

text: deep underwater confined environment

characteristic: broad-scale environmental context

text: not provided

characteristic: collection date

text: Individual airborne biological exposome in a unique deep underwater confined environment

text: air

characteristic: environmental medium

text: China

text: not provided

unit: DD

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: A sampler worn on the chest

characteristic: local environmental context

text: air metagenome

text: A sampler worn on the chest

characteristic: project name

text: air metagenome

characteristic: title


characteristic: ENA first public

text: Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain

characteristic: INSDC center name

text: public

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: Protocols: Animals were sacrificed by decapitation. Striatum was cold extracted and stored at -80C prior to RNA isolation.  RNA was isolated from the striatum samples using the RNeasy Lipid Tissue Mini kit (Qiagen, Barcelona, Spain) following the manufacturer’s instructions, including the optional DNase I step. Once RNA was isolated, samples were stored at −80°C following library preparation. RNA concentration and RNA integrity number (RIN) was assessed using Nanodrop and Bioanalyzer (Centre for Genomic Regulation, Barcelona, Spain).  Libraries were prepared using the TruSeq stranded mRNA Library Prep (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.  Briefly, 1000 or 500 ng of total RNA were used for poly(A)-mRNA selection using poly-T oligo attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis. Then, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers.  After that, second strand cDNA was synthesized, removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA using DNA Polymerase I and RNase H. These cDNA fragments, then had the addition of a single 'A' base to the 3’ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation. A corresponding single T nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragments. Subsequent ligation of the multiple indexing adapter to the ends of the ds cDNA was done.  Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed with a PCR Primer Cocktail that anneals to the ends of the adapters.  Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref: 5067-1504 or ref: DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (REF. 07960204001, Roche) prior to the amplification with Illumina’s cBot Libraries were prepared using the TruSeq stranded mRNA Library Prep (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.  Briefly, 1000 or 500 ng of total RNA were used for poly(A)-mRNA selection using poly-T oligo attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis. Then, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers.  After that, second strand cDNA was synthesized, removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA using DNA Polymerase I and RNase H. These cDNA fragments, then had the addition of a single 'A' base to the 3’ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation. A corresponding single T nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragments. Subsequent ligation of the multiple indexing adapter to the ends of the ds cDNA was done.  Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed with a PCR Primer Cocktail that anneals to the ends of the adapters.  Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref: 5067-1504 or ref: DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (REF. 07960204001, Roche) prior to the amplification with Illumina’s cBot.

characteristic: description

text: adult

characteristic: developmental stage

text: Parkinson’s disease

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not collected

text: A53T virus

characteristic: infect

text: not applicable

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: adult

text: normal

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: control

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male