status: KILLED

text: Wellcome Sanger Institute

text: killed

tag: Namespace:Wellcome Sanger Institute

text: 70 to 75

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

text: Protocols: For adult samples, fresh mucosal tissue were excised within 60 minutes of circulatory arrest and colon tissue preserved in University of Wisconsin (UW) organ preservation solution (Belzer UW® Cold Storage Solution, Bridge to Life, USA) and mLN stored in saline at 4°C until processing. All tissues were processed immediately after isolation using consistent protocols with variation in enzymatic digestion strength (dx.doi.org/10.17504/protocols.io.q3xdypn). Cells were counted using NucleoCounter NC-200 and Via1-Cassette and diluted in 0.04% BSA in PBS to a concentration for capture of to attain 8,000-10,000 cells per well according the the 10x Genomics manufacturers protocol. Cells were loaded into the 10x Chromium Controller according to the manufacturer's protocol at a concentration that would attain between 8,000-10,000 cells/chip position. 10x Genomics VDJ libraries were generated from the 5’ 10x Genomics Chromium cDNA libraries as detailed in the manufacturer's protocol.

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: caecum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 70 to 75

text: ArrayExpress

text: B cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: killed

text: 70 to 75

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: caecum

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: ascending colon

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: descending colon

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: sigmoid colon

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: rectum

text: Homo sapiens

text: male

characteristic: title


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: B cell

characteristic: cell type

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: duodenum

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: jejunum

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 65 to 70

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: ileum

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 25 to 30

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: male

characteristic: title


text: Wellcome Sanger Institute

text: killed

text: 25 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: ileum

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 25 to 30

text: ArrayExpress

text: B cell

text: human

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 25 to 30

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

characteristic: organism part

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 25 to 30

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: caecum

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

text: killed

text: 25 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: mesenteric lymph node

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 60 to 65

text: ArrayExpress

text: B cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: jejunum

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 60 to 65

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: caecum

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 60 to 65

text: ArrayExpress

text: B cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

characteristic: organism part

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: killed

text: 60 to 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: ascending colon

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 60 to 65

text: ArrayExpress

text: B cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: descending colon

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 60 to 65

text: ArrayExpress

text: B cell

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 60 to 65

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: killed

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 25 to 30

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 60 to 65

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: veniform appendix

text: Homo sapiens

text: female

characteristic: title


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: ascending colon

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

text: 60 to 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ascending colon

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: caecum

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 25 to 30

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: caecum

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 70 to 75

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: caecum

text: Homo sapiens

text: female

characteristic: title


text: Wellcome Sanger Institute

text: killed

text: 60 to 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: caecum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: descending colon

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 60 to 65

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: descending colon

characteristic: organism part

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: duodenum

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

text: killed

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: ileum

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 25 to 30

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: ileum

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: jejunum

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 60 to 65

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: jejunum

characteristic: organism part

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: killed

text: 25 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: mesenteric lymph node

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 70 to 75

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: mesenteric lymph node

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: rectum

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

text: 25 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: killed

text: 70 to 75

text: ArrayExpress

text: T cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: killed

text: 65 to 70

text: ArrayExpress

text: T cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: male

characteristic: title


text: Wellcome Sanger Institute

characteristic: INSDC last update

text: killed

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 25 to 30

text: ArrayExpress

text: T cell

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: killed

text: 70 to 75

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: human

characteristic: common name

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: transverse colon

text: Homo sapiens

text: female


status: PUBLIC

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-abcam_1

tag: Namespace:Berlin Institute for Medical Systems Biology

text: ArrayExpress

text: neuron

text: house mouse

text: Protocols: mESC culture and generation of Ascl1-induced neurons was performed as described previously (Zappulo, et al. 2017). Total RNA was extracted from Ascl1-induced neurons using the RNeasy Plus Universal Midikit (Qiagen #73442) according to manufacturer instructions. m6A-RIP was performed with two different m 6 A-specific antibodies (Abcam 151230 and SySy 202003). m 6 A-RIP was performed in triplicates and using input of 10 µg total RNA, 5 pg of spike-in, 50 µl Protein-G-Dynabeads (ThermoFisher 1004D) and either 15 µg of Abcam antibody or 8.5 µg of SySy antibody. For fragmented m 6 A-RIP, 15 µg of total input RNA, 75 µl dynabeads and 13 µg SySy antibody was used.For each m6A-RIP, Dynabeads were washed twice with ice-cold IP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% NP-40, 5 mM EDTA) and then incubated with the respective m6A-specific antibody in 1ml IP buffer with gentle rotation overnight at 4°C. The next day the beads were washed once with 1ml ice-cold IP buffer. Input RNA was heated for 2 min at 80°C and immediately chilled on ice for 5 min. The RNA was added to the antibody-bound beads in a total volume of 1ml IP buffer including 10 µl RNasin (Promega N2615) and rotated for 3 hours at 4°C. The beads were then collected on a magnet for 1 min and the supernatant was carefully removed and collected in a separate tube (= flowthrough fraction). Subsequently, a series of washing steps with several washing buffers was performed. For each washing step, the beads were resuspended in 1 ml buffer and incubated for 3 min at room temperature with gentle shaking, followed by collection of the beads on a magnet for 1 min. The beads were washed twice in 1ml IP buffer, once in 1 ml low salt buffer (0.25x SSPE, 1mMEDTA, 0.05% Tween, 37.5 mM NaCl), once in 1ml high salt buffer (0.25x SSPE, 1mM EDTA, 0.05% Tween, 137.5 mM NaCl) and twice in 1ml TE (10mM TRIS, 1mM EDTA, pH 8.0) containing 0.05% Tween. Following the wash steps the RNA was eluted by incubation for 1 hour at room temperature in 200 µl elution buffer containing 3 mg/ml m6A-nucleoside (Sigma M2780 or SantaCruz sc-215524). The elution step was done twice. The two eluates were pooled and the RNA was extracted using Phenol/Chloroform/Isoamylalcohol. The RNA was precipitated overnight at -20°C with 1/10 volume of 3M sodium acetate pH 5.2, 2.5 volumes of 100% EtOH and 2 µl GlycoBlue (ThermoFisher AM9516) as coprecipitant. After precipitation the RNA was washed twice with 0.5 ml ice-cold 70% EtOH, air-dried and resuspended in 20 µl water. RNA concentration was measured using Qubit. For each library, 100 ng of RNA was mixed with ERCC RNA spike-ins and subjected to library preparation using the TrueSeq stranded total RNA library prep kit (Illumina RS-122-2201) including Ribo-Zero ribosomal RNA depletion according to the manufacturer’s recommendations. In case when RNA input was fragmented before IP (fragmented m6A-RIP-seq), the fragmentation step of the library preparation protocol was omitted.

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Berlin Institute for Medical Systems Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-abcam_2

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-abcam_3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

characteristic: cell type

text: house mouse

characteristic: common name

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-sysy_1

text: ArrayExpress

text: neuron

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-sysy_2

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9542:Flow_m6ARIP_unfragmented-sysy_3

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

characteristic: cell type

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9542:Input_totalRNA_unfragmented_1

text: ArrayExpress

text: neuron

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9542:Input_totalRNA_unfragmented_2

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9542:Input_totalRNA_unfragmented_3

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9542:IP_m6ARIP_fragmented-abcam_1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

characteristic: cell type

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9542:IP_m6ARIP_fragmented-abcam_2

text: ArrayExpress

text: neuron

text: house mouse

characteristic: common name

characteristic: description

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9542:IP_m6ARIP_fragmented-abcam_3

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9542:IP_m6ARIP_unfragmented-abcam_1

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Mus musculus


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9542:IP_m6ARIP_unfragmented-abcam_2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9542:IP_m6ARIP_unfragmented-abcam_3

text: ArrayExpress

text: neuron

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9542:IP_m6ARIP_unfragmented-sysy_1

text: ArrayExpress

text: neuron

text: house mouse

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9542:IP_m6ARIP_unfragmented-sysy_2

text: ArrayExpress

text: neuron

text: house mouse

text: Protocols: mESC culture and generation of Ascl1-induced neurons was performed as described previously (Zappulo, et al. 2017). Total RNA was extracted from Ascl1-induced neurons using the RNeasy Plus Universal Midikit (Qiagen #73442) according to manufacturer instructions. m6A-RIP was performed with two different m 6 A-specific antibodies (Abcam 151230 and SySy 202003). m 6 A-RIP was performed in triplicates and using input of 10 µg total RNA, 5 pg of spike-in, 50 µl Protein-G-Dynabeads (ThermoFisher 1004D) and either 15 µg of Abcam antibody or 8.5 µg of SySy antibody. For fragmented m 6 A-RIP, 15 µg of total input RNA, 75 µl dynabeads and 13 µg SySy antibody was used.For each m6A-RIP, Dynabeads were washed twice with ice-cold IP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% NP-40, 5 mM EDTA) and then incubated with the respective m6A-specific antibody in 1ml IP buffer with gentle rotation overnight at 4°C. The next day the beads were washed once with 1ml ice-cold IP buffer. Input RNA was heated for 2 min at 80°C and immediately chilled on ice for 5 min. The RNA was added to the antibody-bound beads in a total volume of 1ml IP buffer including 10 µl RNasin (Promega N2615) and rotated for 3 hours at 4°C. The beads were then collected on a magnet for 1 min and the supernatant was carefully removed and collected in a separate tube (= flowthrough fraction). Subsequently, a series of washing steps with several washing buffers was performed. For each washing step, the beads were resuspended in 1 ml buffer and incubated for 3 min at room temperature with gentle shaking, followed by collection of the beads on a magnet for 1 min. The beads were washed twice in 1ml IP buffer, once in 1 ml low salt buffer (0.25x SSPE, 1mMEDTA, 0.05% Tween, 37.5 mM NaCl), once in 1ml high salt buffer (0.25x SSPE, 1mM EDTA, 0.05% Tween, 137.5 mM NaCl) and twice in 1ml TE (10mM TRIS, 1mM EDTA, pH 8.0) containing 0.05% Tween. Following the wash steps the RNA was eluted by incubation for 1 hour at room temperature in 200 µl elution buffer containing 3 mg/ml m6A-nucleoside (Sigma M2780 or SantaCruz sc-215524). The elution step was done twice. The two eluates were pooled and the RNA was extracted using Phenol/Chloroform/Isoamylalcohol. The RNA was precipitated overnight at -20°C with 1/10 volume of 3M sodium acetate pH 5.2, 2.5 volumes of 100% EtOH and 2 µl GlycoBlue (ThermoFisher AM9516) as coprecipitant. After precipitation the RNA was washed twice with 0.5 ml ice-cold 70% EtOH, air-dried and resuspended in 20 µl water. RNA concentration was measured using Qubit. For each library, 100 ng of RNA was mixed with ERCC RNA spike-ins and subjected to library preparation using the TrueSeq stranded total RNA library prep kit (Illumina RS-122-2201) including Ribo-Zero ribosomal RNA depletion according to the manufacturer’s recommendations. In case when RNA input was fragmented before IP (fragmented m6A-RIP-seq), the fragmentation step of the library preparation protocol was omitted.

text: embryo

text: normal

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: embryonic stem cell

text: Mus musculus


text: Berlin Institute for Medical Systems Biology

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9542:IP_m6ARIP_unfragmented-sysy_3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: Zebrafish_Whole_Pancreas_H3K27ac_ChIP-seq_replicate1

text: zebrafish

characteristic: common name

text: Adult zebrafish whole pancreas H3K27ac ChIP-seq replicate 1

text: Danio rerio

text: Danio rerio

text: whole pancreas

characteristic: tissue type

text: Zebrafish whole pancreas H3K27ac ChIP-seq replicate 1


characteristic: ENA-LAST-UPDATE

text: public

text: Zebrafish_Whole_Pancreas_H3K27ac_ChIP-seq_replicate2

text: zebrafish

text: Adult zebrafish whole pancreas H3K27ac ChIP-seq replicate 2

characteristic: description

text: Danio rerio

text: Danio rerio

text: whole pancreas

text: Zebrafish whole pancreas H3K27ac ChIP-seq replicate 2


text: public

text: Zebrafish_Whole_Pancreas_H3K4me3_HiChIP-seq_replicate1

text: zebrafish

text: Adult zebrafish whole pancreas H3K4me3 HiChIP-seq replicate 1

text: Danio rerio

text: Danio rerio

text: whole pancreas

text: Zebrafish Whole Pancreas H3K4me3 HiChIP-seq replicate 1

characteristic: title


characteristic: External Id

text: public

text: Zebrafish_Whole_Pancreas_H3K4me3_HiChIP-seq_replicate2

text: zebrafish

text: Adult zebrafish whole pancreas H3K4me3 HiChIP-seq replicate 2

text: Danio rerio

text: Danio rerio

text: whole pancreas

text: Zebrafish Whole Pancreas H3K4me3 HiChIP-seq replicate 2


characteristic: INSDC center name

text: public

text: ArrayExpress

text: Ascl1-induced neurons (iNeurons)

characteristic: cell line

text: neuron

characteristic: cell type

text: house mouse

text: Protocols: Ascl1 WT cells and dnCAF1 cells were differentiated 2days in AK media and seeded on poly-L- ornithine and laminine coated 24-well dish in monolayer media + doxycycline (3ug/mL). After differentiation with dox for 3days, media was exchanged with fresh monolayer media containing 5uM ponasteroneA, 3ug/mL doxycycline and 200uM 4SU. After 24hours, the media was exchanged again with fresh monolayer media containing 5uM ponasteroneA, 3ug/mL doxycycline and 20mM Uridine. Cells were collected in Trifast 0/2/4/8/16 hours after exchanging with 20mM uridine media. Three wells were collected at each timepoint to make three replicates. RNA was extracted from Trifast lysate and alkylated using SLAMseq Kinetics Kit (Lexogen 062.24). QuantSeq 3‘ mRNA-Seq Library Prep Kit (REV) for Illumina with Custom Sequencing (016.24) Input: 250-500ng total RNA

text: dominant negative CAF1 mutant

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Ascl1-induced neurons (iNeurons)

text: neuron

text: house mouse

text: WT

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


E-MTAB-9547:G-2 CAF 1

text: public

characteristic: SRA accession

text: E-MTAB-9547:G-2 CAF 1

tag: Namespace:Department of  Gynecology and Obstetrics, University Medical Center Gottingen

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mammary gland epithelial cell

text: house mouse

text: Protocols: G-2 cells were treated with CAF (312,5 ng/ml cyclophosphamide, 15,6 ng/ml doxorubicin and 312,5 ng/ml 5-FU) in 10 cm plates for 48 hours in biological triplicates. Total RNA was extracted from G-2 cells with Qiazol (Qiagen) following the manufacturer's recommendations. mRNA sequencing libraries were generated with the NEXTflex™ Rapid Illumina Directional Kit according to the manufacturer’s instructions. The size of the generated libraries was estimated on High Sensitivity DNA chip (Agilent) using a Bioanalyser 2100 (Agilent).

text: triple-negative breast cancer

characteristic: disease

text: Mus musculus

text: Mus musculus

text: breast

characteristic: organism part

characteristic: replicate

text: Mus musculus

text: BALB/c, WAP-T

characteristic: strain

text: G-2 CAF 1


E-MTAB-9547:G-2 CAF 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Department of Gynecology and Obstetrics, University Medical Center Gottingen

text: public

text: E-MTAB-9547:G-2 CAF 2

text: ArrayExpress

text: mammary gland epithelial cell

text: house mouse

characteristic: common name

characteristic: description

text: triple-negative breast cancer

text: Mus musculus

text: Mus musculus

text: breast

text: Mus musculus

text: BALB/c, WAP-T

text: G-2 CAF 2

characteristic: title


E-MTAB-9547:G-2 CAF 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9547:G-2 CAF 3

text: ArrayExpress

characteristic: cell line

text: mammary gland epithelial cell

characteristic: cell type

text: house mouse

text: triple-negative breast cancer

text: Mus musculus

text: Mus musculus

text: breast

text: Mus musculus

text: BALB/c, WAP-T

text: G-2 CAF 3


E-MTAB-9547:G-2 Vehicle 1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9547:G-2 Vehicle 1

characteristic: Submitter Id

text: ArrayExpress

text: mammary gland epithelial cell

text: house mouse

text: triple-negative breast cancer

text: Mus musculus

characteristic: organism

text: Mus musculus

text: breast

text: Mus musculus

text: BALB/c, WAP-T

text: G-2 Vehicle 1


E-MTAB-9547:G-2 Vehicle 2

text: public

text: E-MTAB-9547:G-2 Vehicle 2

text: ArrayExpress

characteristic: broker name

text: mammary gland epithelial cell

text: house mouse

text: triple-negative breast cancer

characteristic: disease

text: Mus musculus

text: Mus musculus

text: breast

characteristic: organism part

characteristic: replicate

text: Mus musculus

text: BALB/c, WAP-T

characteristic: strain

text: G-2 Vehicle 2


E-MTAB-9547:G-2 Vehicle 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9547:G-2 Vehicle 3

text: ArrayExpress

text: mammary gland epithelial cell

text: house mouse

characteristic: common name

characteristic: description

text: triple-negative breast cancer

text: Mus musculus

text: Mus musculus

text: breast

text: Mus musculus

text: BALB/c, WAP-T

text: G-2 Vehicle 3


E-MTAB-9556:Ncol3mOrange2 Neg R1

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9556:Ncol3mOrange2 Neg R1

tag: Namespace:Sars Centre for Marine Molecular Biology, University of Bergen

text: ArrayExpress

text: NvNcol3::mOrange2 Negative cells

text: starlet sea anemone

text: Protocols: FACS sorting were performed as previously described (Torres-Mendez et al. 2019). Briefly, animals were dissociated in 0.25% Trypsin (Gibco, 27250018) in Ca- Mg- free Nematostella media (CMFNM) (154 mM NaCl, 3.6 mM KCl, 2.4 mM Na2SO4, 0.7 mM NaHCO3) supplemented with 6.6 mM EDTA , pH 7.6-7.8. Cells were centrifuged at 800 g for 10 minutes, resuspended in ice cold 0.5% BSA in CMFNM (pH 7.6-7.8), filtered through a 40 μM filter and stained with Hoechst 33342 (Thermo Fisher Scientific, 62249) at a 60 μg/ml at RT for 30 minutes. Samples were then diluted 1:1 with ice cold 0.5% BSA/CMFNM and stained with 60 μl/ml 7-AAD (BD, 559925) for > 20 minutes on ice. Sorting was carried out on a BD FACSAria II with a 100 μm nozzle. RNA extraction was performed as previously published (Torres-Mendez et al. 2019). Cells were sorted directly into 0.5% BSA/ CMFNM at 4°C and centrifuged at 800 g for 10 minutes at 4°C. Most of the liquid was removed and 3 volumes of TRIzol LS reagent (Invitrogen, 10296028) was added. Samples were vortexed extensively and incubated at RT for 5 minutes before being flash frozen and stored at -80°C. The samples were processed using Direct-zol RNA MicroPrep columns (Zymo Research, R2060) including on column DNase digestion. cDNA was prepared from 400 pg of total RNA using the Smart-Seq 2 method with 16 pre-amplification PCR cycles (Picelli et al. 2014). NGS libraries were prepared using the home-made tagmentation-based method (Hennig et al. 2018). Briefly, 125 ng of cDNA was tagmented using home-made Tn5 loaded with annealed linker oligonucleotides for 3 minutes at 55°C. Reactions were inactivated by adding 1.25 ml of 0.2% SDS and incubation for 5 minutes at RT. Indexing and amplification was done using the KAPA HiFi HotStart PCR kit (Sigma-Aldrich, KK1508) with Index oligonucleotides (sequences were adapted from Illumina).

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Neg R1

characteristic: title


E-MTAB-9556:Ncol3mOrange2 Neg R2

text: Sars Centre for Marine Molecular Biology, University of Bergen

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9556:Ncol3mOrange2 Neg R2

text: ArrayExpress

text: NvNcol3::mOrange2 Negative cells

characteristic: cell type

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Neg R2


E-MTAB-9556:Ncol3mOrange2 Neg R3

text: public

text: E-MTAB-9556:Ncol3mOrange2 Neg R3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: NvNcol3::mOrange2 Negative cells

text: starlet sea anemone

text: Nematostella vectensis

characteristic: organism

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Neg R3


E-MTAB-9556:Ncol3mOrange2 Neg R4

text: public

text: E-MTAB-9556:Ncol3mOrange2 Neg R4

text: ArrayExpress

text: NvNcol3::mOrange2 Negative cells

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Neg R4


E-MTAB-9556:Ncol3mOrange2 Pos R1

text: public

text: E-MTAB-9556:Ncol3mOrange2 Pos R1

text: ArrayExpress

text: NvNcol3::mOrange2 Positve cells

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Pos R1


E-MTAB-9556:Ncol3mOrange2 Pos R2

text: public

text: E-MTAB-9556:Ncol3mOrange2 Pos R2

text: ArrayExpress

text: NvNcol3::mOrange2 Positve cells

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Pos R2


E-MTAB-9556:Ncol3mOrange2 Pos R3

text: public

text: E-MTAB-9556:Ncol3mOrange2 Pos R3

text: ArrayExpress

text: NvNcol3::mOrange2 Positve cells

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Pos R3


E-MTAB-9556:Ncol3mOrange2 Pos R4

text: public

text: E-MTAB-9556:Ncol3mOrange2 Pos R4

text: ArrayExpress

text: NvNcol3::mOrange2 Positve cells

text: starlet sea anemone

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Ncol3mOrange2 Pos R4


text: public

text: Zebrafish_Endocrine_Pancreas_RNA-seq_replicate1

text: zebrafish

text: Adult zebrafish endocrine pancreas (principal islet) RNA-seq raw reads replicate1

text: Danio rerio

text: Danio rerio

text: endocrine pancreas (principal islet)

characteristic: tissue type

text: Zebrafish Endocrine Pancreas RNA-seq replicate1


characteristic: ENA-CHECKLIST

text: public

text: Zebrafish_Endocrine_Pancreas_RNA-seq_replicate2

text: zebrafish

text: Adult zebrafish endocrine pancreas (principal islet) RNA-seq raw reads replicate2

text: Danio rerio

text: Danio rerio

text: endocrine pancreas (principal islet)

text: Zebrafish Endocrine Pancreas RNA-seq replicate2


characteristic: ENA-FIRST-PUBLIC

text: public

text: Zebrafish_Endocrine_Pancreas_RNA-seq_replicate3

text: zebrafish

text: Adult zebrafish endocrine pancreas RNA-seq replicate3 raw reads

text: Danio rerio

text: Danio rerio

text: endocrine pancreas (principal islet)

text: Zebrafish Endocrine Pancreas RNA-seq replicate3


characteristic: ENA-LAST-UPDATE

text: public

text: Zebrafish_Endocrine_Pancreas_RNA-seq_replicate4

text: zebrafish

text: Adult zebrafish endocrine pancreas RNA-seq replicate4 raw reads

text: Danio rerio

text: Danio rerio

text: endocrine pancreas (principal islet)

text: Zebrafish Endocrine Pancreas RNA-seq replicate4


text: public

text: zebrafish

characteristic: common name

text: Adult zebrafish muscle RNA-seq replicate1 raw reads

text: Danio rerio

text: Danio rerio

text: muscle

text: Zebrafish Muscle RNA-seq replicate1


text: public

text: zebrafish

text: Adult zebrafish muscle RNA-seq replicate2 raw reads

characteristic: description

text: Danio rerio

text: Danio rerio

text: muscle

text: Zebrafish Muscle RNA-seq replicate2


characteristic: External Id

text: public

text: Zebrafish_Whole_Pancreas_RNA-seq_replicate1

text: zebrafish

text: Adult zebrafish whole pancreas RNA-seq replicate1 raw reads

text: Danio rerio

text: Danio rerio

text: whole pancreas

text: Zebrafish Whole Pancreas RNA-seq replicate1


characteristic: INSDC center name

text: public

text: Zebrafish_Whole_Pancreas_RNA-seq_replicate2

text: zebrafish

text: Adult zebrafish whole pancreas RNA-seq replicate2 raw reads

text: Danio rerio

text: Danio rerio

text: whole pancreas

text: Zebrafish Whole Pancreas RNA-seq replicate2


text: SAN DIEGO STATE UNIV

characteristic: INSDC first public

text: public

tag: Namespace:SAN DIEGO STATE UNIV

characteristic: collection date

text: house mouse

text: gut

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: 117.2340 W

unit: DD

characteristic: geographic location (latitude)

text: 32.8801 N

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Mus musculus

text: Shotgun gut metagenome of letrozole induced PCOS mouse model

characteristic: project name

text: Mus musculus

text: Illumina pair-end sequencing

characteristic: sequencing method

text: Shotgun gut metagenomes


E-MTAB-9562:Planula Control 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9562:Planula Control 1

tag: Namespace:Sars Centre for Marine Molecular Biology

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: starlet sea anemone

text: Protocols: We performed an NvLsd1GFP/- x NvLsd1GFP/- cross. 75% of the animals have at least one copy of the NvLsd1GFP allele, hereafter called control, and the homozygous mutant animals are GFP negative, hereafter NvLsd-/-. Anaimals were separated based on whether they were GFP negative or positive and 50 animals were used per sample. 50 animals per sample were lysed in 500 μl TRIzol reagent (Invitrogen, 15596026) by vortexing extensively and incubated at RT for 5 minutes. 100 μl of chloroform was added and mixed vigorously and the aqueous component was isolated using MaXtract High Density tubes (Qiagen, 129046) using the manufacturers protocol. One volume of 100% Ethanol was added to the aqueous phase. This was then processed using an RNeasy Micro Kit (Qiagen, 74004) using the manufacturers protocol including on column DNase digestion using the RNase-Free DNase Set (Qiagen, 79254). RNA quality was assessed using an RNA 6000 Pico Kit (Aligent, 5067-1513) and concentration determined using the Qubit™ RNA HS assay kit (Invitrogen, Q32852). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L), with following changes: 25ng RNA input, 1/100 adaptor dilution, 14 PCR cycles.

text: 4 day old larva

characteristic: developmental stage

text: Control (NvLsd1GFP/- and NvLsd1GFP/GFP )

characteristic: genotype

text: Nematostella vectensis

characteristic: organism

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Control 1

characteristic: title


E-MTAB-9562:Planula Control 2

characteristic: External Id

text: Sars Centre for Marine Molecular Biology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9562:Planula Control 2

text: ArrayExpress

text: starlet sea anemone

characteristic: common name

characteristic: description

text: 4 day old larva

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Control 2


E-MTAB-9562:Planula Control 3

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-9562:Planula Control 3

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Control 3


E-MTAB-9562:Planula Control 4

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9562:Planula Control 4

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Control 4


E-MTAB-9562:Planula Mutant 1

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-9562:Planula Mutant 1

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Mutant 1


E-MTAB-9562:Planula Mutant 2

characteristic: INSDC last update

text: public

text: E-MTAB-9562:Planula Mutant 2

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Mutant 2


E-MTAB-9562:Planula Mutant 3

text: public

characteristic: INSDC status

text: E-MTAB-9562:Planula Mutant 3

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Mutant 3


E-MTAB-9562:Planula Mutant 4

text: public

characteristic: SRA accession

text: E-MTAB-9562:Planula Mutant 4

text: ArrayExpress

text: starlet sea anemone

text: 4 day old larva

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Planula Mutant 4


E-MTAB-9562:Polyp Control 1

text: public

text: E-MTAB-9562:Polyp Control 1

characteristic: Submitter Id

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Control 1


E-MTAB-9562:Polyp Control 2

text: public

text: E-MTAB-9562:Polyp Control 2

text: ArrayExpress

characteristic: broker name

text: starlet sea anemone

text: primary polyp

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Control 2


E-MTAB-9562:Polyp Control 3

text: public

text: E-MTAB-9562:Polyp Control 3

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

characteristic: developmental stage

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Control 3


E-MTAB-9562:Polyp Control 4

text: public

text: E-MTAB-9562:Polyp Control 4

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

characteristic: genotype

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Control 4


E-MTAB-9562:Polyp Mutant 1

text: public

text: E-MTAB-9562:Polyp Mutant 1

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

text: NvLsd-/-

text: Nematostella vectensis

characteristic: organism

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Mutant 1


E-MTAB-9562:Polyp Mutant 2

text: public

text: E-MTAB-9562:Polyp Mutant 2

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Mutant 2

characteristic: title


E-MTAB-9562:Polyp Mutant 3

characteristic: External Id

text: public

text: E-MTAB-9562:Polyp Mutant 3

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Mutant 3


E-MTAB-9562:Polyp Mutant 4

characteristic: INSDC center name

text: public

text: E-MTAB-9562:Polyp Mutant 4

text: ArrayExpress

text: starlet sea anemone

text: primary polyp

text: NvLsd-/-

text: Nematostella vectensis

text: Nematostella vectensis

text: Nematostella vectensis

text: Polyp Mutant 4


text: ISTITUTO ITALIANO DI TECNOLOGIA

characteristic: INSDC first public

text: public

tag: Namespace:ISTITUTO ITALIANO DI TECNOLOGIA

text: neural progenitor cells

characteristic: cell type

text: western European house mouse

text: time 0 replica 1

text: adult

characteristic: dev stage

text: Mus musculus domesticus

text: Mus musculus domesticus


characteristic: ENA-CHECKLIST

text: ISTITUTO ITALIANO DI TECNOLOGIA

text: public

text: neural progenitor cells

text: western European house mouse

characteristic: common name

text: time 0 replica 2

characteristic: description

text: adult

text: Mus musculus domesticus

text: Mus musculus domesticus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ISTITUTO ITALIANO DI TECNOLOGIA

characteristic: INSDC last update

text: public

text: neural progenitor cells

text: western European house mouse

text: time 4 replica 2

text: adult

text: Mus musculus domesticus

text: Mus musculus domesticus


text: ISTITUTO ITALIANO DI TECNOLOGIA

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: neural progenitor cells

text: western European house mouse

text: time 7 replica 1

text: adult

text: Mus musculus domesticus

text: Mus musculus domesticus


text: ISTITUTO ITALIANO DI TECNOLOGIA

text: public

text: neural progenitor cells

text: western European house mouse

text: time 7 replica 2

text: adult

text: Mus musculus domesticus

text: Mus musculus domesticus


text: public

tag: Namespace:Department of Plant and Microbial Biology University of Zurich

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: The following tissue was harvested for the three different stages: i) ovaries two days after emasculation (style and stigma were removed), ii) developing seeds 1-2 days after pollination (dissected from siliques), and iii) developing seeds 4 days after pollination (dissected from siliques). Three independent biological replicates were generated for each tissue/genotype combination. For each replicate, the isolated tissue were frozen in liquid nitrogen, ground to a fine powder using a pestle and incubated for 10 minutes in 450 µl of a solution containing 2% CTAB, 100 mM Tris-HCl pH 8.0, 25 mM EDTA, 2M NaCl and 2% ß-mercaptoethanol. This suspension was then mixed with ice-cold chloroform was centrifuged 15 minutes at 16000 g. The upper phase was collected and mixed with 150µl of a 8M LiCl solution, incubated at -20 ºC for one hour and centrifuged 30 minutes at 16000 g. The RNA pellet was washed with 70% ethanol and resuspended in 30 µl RNAse free water and quantified using the Qubit. The Turbo DNA free kit (Ambion AM1907) was used to remove DNA. Total RNA samples were polyA enriched and reverse-transcribed into double stranded cDNA. A total of18 libraries were generated using the TruSeq RNA Sample Prep Kit (Illumina) using 1µg total RNA. Libraries were validated using the ddPCR Library quantification kit for Illumina TruSeq (Biorad 186-3040): Amplicons from all the libraries had approximately the same size and were at a 60-120nM concentration range.

text: stage 12 to 13

characteristic: developmental stage

text: Landsberg ecotype

characteristic: ecotype

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: plant ovary

characteristic: organism part

text: Arabidopsis thaliana


characteristic: External Id

text: Department of Plant and Microbial Biology University of Zurich

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: thale cress

text: stage 12 to 13

text: Landsberg ecotype

text: wild type genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: plant ovary

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: thale cress

characteristic: common name

characteristic: description

text: 1 to 2 days after pollination

text: Landsberg ecotype

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: ArrayExpress

text: thale cress

text: 4 days after pollination

text: Landsberg ecotype

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: stage 12 to 13

text: Landsberg ecotype

text: mea homozygous knockout

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: plant ovary

text: Arabidopsis thaliana


text: public

text: ArrayExpress

characteristic: broker name

text: thale cress

text: 1 to 2 days after pollination

characteristic: developmental stage

text: Landsberg ecotype

characteristic: ecotype

text: mea homozygous knockout

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana


characteristic: External Id

text: public

text: ArrayExpress

text: thale cress

text: 4 days after pollination

text: Landsberg ecotype

text: mea homozygous knockout

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

characteristic: organism part

text: Arabidopsis thaliana


E-MTAB-9579:Chen liu

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9579:Chen liu

tag: Namespace:Tongji University; Shanghai East Hospital

characteristic: age

text: ArrayExpress

text: human

text: Protocols: Genomic DNA was extracted from whole blood using TIANamp Blood DNA Kit (Tiangen Biotech, Beijing, China), which was further treated with EpiTect Fast DNA Bisulfite Kit (QIAGEN, Hilden, Germany) for bisulfite conversion. The converted DNA was PCR-amplified with primer sequences designed to cover the CpGs in two promoter regions denoted as “Promoter 1” and “Promoter 2” The PCR products were gel- and column-purified and used for DNA library preparation. The library was prepared with KAPA HTP Library Preparation Kit (KAPA Biosystems, Wilmington, MA) according to the manufacturer’s protocol.

text: short stature

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: sex

text: Chen liu


E-MTAB-9579:Jiarui Lin

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Tongji University; Shanghai East Hospital

text: public

text: E-MTAB-9579:Jiarui Lin

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: short stature

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: Jiarui Lin

characteristic: title


E-MTAB-9579:Jiaxin Liu

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9579:Jiaxin Liu

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: Jiaxin Liu


E-MTAB-9579:Siyuan Huang

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-9579:Siyuan Huang

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male

text: Siyuan Huang


E-MTAB-9579:Xinyu Chen

characteristic: INSDC first public

text: public

text: E-MTAB-9579:Xinyu Chen

characteristic: age

text: ArrayExpress

text: human

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: Xinyu Chen


E-MTAB-9579:Ye Zhang

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-9579:Ye Zhang

text: ArrayExpress

text: human

text: short stature

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: sex

text: Ye Zhang


Aacetabulum genome1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF OSLO

text: public

text: Aacetabulum genome1

tag: Namespace:UNIVERSITY OF OSLO

text: mermaid's wine glass

characteristic: common name

text: Using droplet MDA to amplify and sequence the genome of the green alga Acetabularia acetabulum

text: Acetabularia acetabulum

text: Acetabularia acetabulum

text: Genome sequencing of Acetabularia acetabulum


Aacetabulum genome6

text: UNIVERSITY OF OSLO

characteristic: INSDC last update

text: public

text: Aacetabulum genome6

text: mermaid's wine glass

characteristic: description

text: Acetabularia acetabulum

text: Acetabularia acetabulum

characteristic: title


Aacetabulum genome7

text: UNIVERSITY OF OSLO

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Aacetabulum genome7

characteristic: Submitter Id

text: mermaid's wine glass

text: Acetabularia acetabulum

text: Acetabularia acetabulum


Aacetabulum genome81

characteristic: External Id

text: UNIVERSITY OF OSLO

characteristic: INSDC center name

text: public

text: Aacetabulum genome81

text: mermaid's wine glass

text: Acetabularia acetabulum

text: Acetabularia acetabulum


Aacetabulum genome91

text: UNIVERSITY OF OSLO

characteristic: INSDC first public

text: public

text: Aacetabulum genome91

text: mermaid's wine glass

text: Acetabularia acetabulum

text: Acetabularia acetabulum


text: INRA-META

text: public

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: saliva

characteristic: host body product

text: human-oral

characteristic: host body site

text: human oral metagenome

text: human oral metagenome

text: human oral metagenome


characteristic: ENA-CHECKLIST

text: INRA-META

text: public

text: United Kingdom

text: stool

text: human-gut

text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: human gut metagenome


characteristic: ENA-FIRST-PUBLIC

text: Institute of Vertebrate Biology, CAS

text: public

tag: Namespace:Institute of Vertebrate Biology, CAS

text: Offspring of a Bombina bombina female (ERS3926743) and a Bombina variegata male (ERS3926742)

text: adult

characteristic: dev stage

text: laboratory cross

characteristic: isolation source

text: Bombina bombina x Bombina variegata

text: Bombina bombina x Bombina variegata

text: female

characteristic: sex

text: F1 female (2016_6_F_12A3)


characteristic: ENA-LAST-UPDATE

text: Institute of Vertebrate Biology, CAS

characteristic: INSDC last update

text: public

characteristic: description

text: adult

text: laboratory cross

text: Bombina bombina x Bombina variegata

text: Bombina bombina x Bombina variegata

text: male

text: F1 male (2016_6_M_07B2)


text: Institute of Vertebrate Biology, CAS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: adult

text: laboratory cross

text: Bombina bombina x Bombina variegata

text: Bombina bombina x Bombina variegata

text: female

text: F1 female (2016_7_F_13A5)

characteristic: title


characteristic: External Id

text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC center name

text: public

tag: Namespace:NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: Submitter Id

characteristic: collection date

text: Sweden

text: diseased

characteristic: host health state

text: Phocoena phocoena

characteristic: host scientific name

characteristic: isolate

text: Porpoise lung

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Porpoise lung isolate 17-VLT2652


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC first public

text: public

text: Sweden

characteristic: geographic location (country and/or sea)

text: diseased

text: Phocoena phocoena

text: Porpoise lung

text: Salmonella enterica subsp. enterica

characteristic: organism

text: Salmonella enterica subsp. enterica

text: Porpoise lung isolate 20-VLT1389


E-MTAB-9584:G-2 CAF H2K27ac rep1

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-9584:G-2 CAF H2K27ac rep1

tag: Namespace:Department of  Gynecology and Obstetrics, University Medical Center Goettingen

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

characteristic: common name

text: Protocols: G-2 cells were treated with CAF (312,5 ng/ml cyclophosphamide, 15,6 ng/ml doxorubicin and 312,5 ng/ml 5-FU) in 15 cm plates for 48 hours in biological triplicates. DNA-Protein complexes were cross-linked with 1% paraformaldehyde in PBS for 20 min at RT. After extraction, the chromatin was sonicated in a Bioruptor Pico (Diagenode) to generate 300-500 bp fragments. 20-30 µg DNA was used per Chromatin Immunoprecipitation reaction. Finally, the immunoprecipitated DNA was purified by phenol-chloroform extraction. ChIP-sequencing libraries were generated using the MicroPlex Library Preparation Kit v2 (Diagenode) along the manufacturers recommendations. The size of the generated libraries was estimated on High Sensitivity DNA chip (Agilent) using a Bioanalyser 2100.

text: breast cancer

characteristic: disease

text: WAP-T1; WAP-mutp53R270H

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: Mus musculus

text: 312.5 ng/ml cyclophosphamide, 15.6 ng/ml doxorubicin and 312.5 ng/ml 5-FU

characteristic: stimulus

text: G-2 CAF H2K27ac rep1


E-MTAB-9584:G-2 CAF H2K27ac rep2

characteristic: External Id

text: Department of Gynecology and Obstetrics, University Medical Center Goettingen

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9584:G-2 CAF H2K27ac rep2

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 CAF H2K27ac rep2

characteristic: title


E-MTAB-9584:G-2 CAF H2K27me3 rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-9584:G-2 CAF H2K27me3 rep1

text: ArrayExpress

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 CAF H2K27me3 rep1


E-MTAB-9584:G-2 CAF H2K27me3 rep2

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-9584:G-2 CAF H2K27me3 rep2

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 CAF H2K27me3 rep2


E-MTAB-9584:G-2 CAF Input rep1

text: public

text: E-MTAB-9584:G-2 CAF Input rep1

text: ArrayExpress

text: house mouse

characteristic: common name

text: breast cancer

characteristic: disease

text: WAP-T1; WAP-mutp53R270H

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: Mus musculus

text: G-2 CAF Input rep1


E-MTAB-9584:G-2 Vehicle H2K27ac rep1

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-9584:G-2 Vehicle H2K27ac rep1

text: ArrayExpress

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 Vehicle H2K27ac rep1


E-MTAB-9584:G-2 Vehicle H2K27ac rep2

text: public

characteristic: SRA accession

text: E-MTAB-9584:G-2 Vehicle H2K27ac rep2

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 Vehicle H2K27ac rep2


E-MTAB-9584:G-2 Vehicle H2K27me3 rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9584:G-2 Vehicle H2K27me3 rep1

text: ArrayExpress

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 Vehicle H2K27me3 rep1

characteristic: title


E-MTAB-9584:G-2 Vehicle H2K27me3 rep2

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: E-MTAB-9584:G-2 Vehicle H2K27me3 rep2

text: ArrayExpress

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 Vehicle H2K27me3 rep2


E-MTAB-9584:G-2 Vehicle Input rep2

characteristic: INSDC last update

text: public

text: E-MTAB-9584:G-2 Vehicle Input rep2

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

text: breast cancer

text: WAP-T1; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: Mus musculus

text: G-2 Vehicle Input rep2


text: public

tag: Namespace:EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

text: ArrayExpress

text: Protocols: WT M129 cells were transformed according to the protocol outlined by Hedreyda et al (Hedreyda et al., 1993). Cells were grown to mid-log phase, identified by the Hayflick media changing from red to orange. The media was decanted and the flask was washed 3x with 10 ml chilled electroporation buffer (EB: 8mM HEPES, 272nM sucrose, pH 7.4). Cells were scraped into 500 µl chilled EB and homogenised via 10x passages through a 25-gauge syringe needle. Aliquots of 50 µl of the homogenised cells were mixed with a pre-chilled 30 µl EB solution containing the 1 pMole of pMTnLox66Cm plasmid DNA. Samples were then kept on ice for 15 mins. Electroporation was done using a Bio-Rad Gene Pulser set to 1250 V, 25 µF and 100Ω. After electroporation, cells were incubated on ice for 15 mins, then recovered into a total of 500 µl Hayflick media and incubated at 37°C for 4 hours. 125 µl of transformed cells were then inoculated into T75 cm2 culture flasks containing 20 ml Hayflick and supplemented with 20 µg/ml chloramphenicol. The transformed cells were grown to mid-log phase, then isolated via pelleting. To ensure the recovery of planktonic cells, the media was transferred to a 50 ml Falcon tube. The flask was then scraped into 500 µl Hayflick, which was added to the Falcon tube with the media. The sample was centrifuged at 10,000 RPM at 4°C for 10 mins to pellet the cells. The supernatant was discarded and the cells resuspended in 500 µl chilled EB. The cells were homogenised via 10x passages through a 25-gauge syringe needle. Aliquots of 50 µl of the homogenised cells were mixed with a pre-chilled 30 µl EB solution containing the 1 pMole of pMTnLox71Tc plasmid DNA, and transformed using the previously described settings. Cells were recovered in the same manner, and 125µl were inoculated into a T75 cm2 flask containing 20 ml Hayflick media supplemented with 2 µg/ml tetracycline and 20 µg/ml chloramphenicol. The transformed cells were again grown to mid-log phase and isolated via the centrifugation method described above. Aliquots of 50 µl of the homogenised cells were mixed with a pre-chilled 30 µl EB solution containing the 1 pMole of pMTnCreGm plasmid DNA, and transformed using the previously described settings. Cells were recovered in the same manner, and 125 µl were inoculated into a T75 cm2 flask containing 20 ml Hayflick media supplemented with 200 µg/ml gentamicin. isolated cells that survived transformation with the pMTnCreGm, 100µl was isolated, and had genetic material isolated via the MasterPure™ genomic DNA purification kit (Lucigen, Cat. No. MC85200). Genomic DNA was fragmented to 300 bp via Covaris sonication. 5’ phosphorylation was undertaken to allow for adapter binding, then 3’ overhangs were filled to create blunt ends. These were then ligated using T4 ligase to create circular fragments, and linear DNA was removed via digest with exonuclease I and lambda exonuclease. Circular DNA was then denatured and amplified using a primer mix containing LE-RE_Lox72, loxloop-6, loxloop-7 and loxloop-8 and a phi29 polymerase to amplify DNA containing a deletion scar. This amplified product was then fragmented again using Covaris to 300 bp and NEBNext Adaptor for Illumina were annealed to the linearised DNA.

text: mutant pool containing 285 unique deletions

characteristic: genotype

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae

text: whole organism

text: Mycoplasma pneumoniae

characteristic: strain


characteristic: External Id

text: public

tag: Namespace:VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, GHENT UNI

text: soil metagenome

text: soil metagenome


text: VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, GHENT UNI

characteristic: INSDC center name

text: public

text: root metagenome

text: root metagenome


text: public

characteristic: INSDC status

text: soil metagenome

text: soil metagenome


text: Cantacuzino NIMMRD

text: public

characteristic: SRA accession

tag: Namespace:Cantacuzino NIMMRD

characteristic: collection date

text: Romania

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: feces

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: SalmEnteritidis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

text: regrowth

characteristic: cohort

text: house mouse

characteristic: common name

text: Protocols: 1x10^6 murine H8N8 mammary carcinoma cells were injected into the right abdominal mammary gland of female nulliparous WAP-T-NP8 mice. Once growing tumors reached a size of approx. 0.5 cm³, the animals were treated with a single intraperitoneal dose CAF chemotherapy (100 mg/kg cyclophosphamide, 5 mg/kg doxorubicin, and 100 mg/kg BW 5FU). Tumor cells were dissociated tumor tissues using the Tumor Dissociation Kit (Miltenyi Biotec) in combination with the gentleMACS Octo Dissociator with heaters (Miltenyi Biotec) according to the manufacturer’s instructions. Finally, the obtained tumor cell suspensions were purified by magnetic-activated cell sorting (MACS) using CD45 (TIL) MicroBeadsin in combination with the Tumor Cell Isolation Kit (Miltenyi Biotec). Total RNA was extracted from H8N8 cells (extracted from tumors growing in syngeneic animals) with Qiazol (Qiagen) following the manufacturer's recommendations. mRNA sequencing libraries were generated with the NEXTflex™ Rapid Illumina Directional Kit according to the manufacturer’s instructions. The size of the generated libraries was estimated on High Sensitivity DNA chip (Agilent) using a Bioanalyser 2100 (Agilent).

characteristic: description

text: adult

characteristic: developmental stage

text: WAP-T-NP8; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

text: BALB/c

characteristic: title

text: 100 mg/kg cyclophosphamide, 5 mg/kg doxorubicin and 100 mg/kg 5-FU

characteristic: treatment


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: remission

text: house mouse

text: adult

text: WAP-T-NP8; WAP-mutp53R270H

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mammary gland

text: neoplasm

text: Mus musculus

text: female

text: BALB/c

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: control

characteristic: cohort

text: house mouse

characteristic: common name

text: adult

text: WAP-T-NP8; WAP-mutp53R270H

text: Mus musculus

text: Mus musculus

text: mammary gland

text: neoplasm

text: Mus musculus

text: female

text: BALB/c


characteristic: External Id

text: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

text: public

text: ArrayExpress

text: Protocols: WT M129 cells were transformed with 1 pMole of the plasmid pMTnLox66Cm, via electroporation. 125 µl of transformed cells were then inoculated into a T75 cm2 culture flask containing 20 ml Hayflick and supplemented with chloramphenicol. The culture was grown to mid-log phase then cells were isolated via centrifugation (Sample R1B1). Aliquots of 50 µl from the previous homogenised cells were mixed with a pre-chilled 30 µl EB solution containing the 1 pMole of pMTnLox71Tc plasmid DNA, and transformed as in the first round. Cells were recovered in the same manner, and 125µl were inoculated into a T75 cm2 flask containing 20 ml Hayflick media supplemented with 2 µg/ml tetracycline and 20 µg/ml chloramphenicol. Genomic DNA was isolated via the MasterPure™ genomic DNA purification kit. Between 10 and 500 ng genomic DNA were fragmented to 200-300 bp using a Covaris S2 instrument. End repair and adaptor ligation was performed using the NEBNext Ultra DNA Library Prep kit for Illumina.

characteristic: description

text: Transformed with pMTnLox66Cm

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae

text: whole organism

characteristic: organism part

text: Mycoplasma pneumoniae

characteristic: title


characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: R1B1 sample pMTnLox71Tc

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae

text: whole organism

text: Mycoplasma pneumoniae


text: INRA-META

text: public

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: stool

characteristic: host body product

text: human-gut

characteristic: host body site

text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: human gut metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRA-META

characteristic: INSDC first public

text: public

text: United Kingdom

text: saliva

text: human-oral

text: human oral metagenome

text: human oral metagenome

text: human oral metagenome


text: MHH

text: public

characteristic: Submitter Id

characteristic: collection date

text: Pseudomonas aeruginosa clone ST235 strain W15Dec14, isolated from a water sample (river)

text: Belgium

text: n. a. (environmental sample)

characteristic: host scientific name

text: W15Dec14, clone ST235 isolate

characteristic: isolate

text: water sample from Woluwe river, Brussels, Belgium

characteristic: isolation source

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa environmental isolate W15Dec14


characteristic: External Id

text: MHH

characteristic: INSDC center name

text: public

text: Pseudomonas aeruginosa clone ST235 strain BW-PB-6, isolated from a burn wound

characteristic: description

text: Poland

text: not provided

characteristic: host health state

text: Homo sapiens

text: BW-PB-6, clone ST235 isolate

text: sample from infected burn wound, Siemianowice Slaskic, Poland

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa burn wound isolate PB6

characteristic: title


text: MHH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Pseudomonas aeruginosa clone ST235 strain BW-PB-7, isolated from a burn wound

text: Poland

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: BW-PB-7, clone ST235 isolate

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa burn wound isolate PB7


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MHH

text: public

text: Pseudomonas aeruginosa clone ST235 strain BW-PB-11, isolated from a burn wound

text: Poland

text: not provided

text: Homo sapiens

text: BW-PB-11, clone ST235 isolate

text: Pseudomonas aeruginosa F469

characteristic: organism

text: Pseudomonas aeruginosa F469

text: P. aeruginosa burn wound isolate PB11


characteristic: ENA-LAST-UPDATE

text: MHH

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Pseudomonas aeruginosa clone ST235 strain BW-PB-12, isolated from a burn wound

text: Poland

text: not provided

text: Homo sapiens

text: BW-PB-12, clone ST235 isolate

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa burn wound isolate PB12


text: MHH

text: public

characteristic: collection date

text: Pseudomonas aeruginosa clone ST235 strain AC-BN-7, isolated from a patient sample (acute infection)

text: Hungary

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: AC-BN-7, clone ST235 isolate

characteristic: isolate

text: patient sample (acute infection) from Budapest, Hungary

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa clnical isolate AC-BN-7


characteristic: External Id

text: MHH

characteristic: INSDC center name

text: public

text: Pseudomonas aeruginosa clone ST235 strain B6065, isolated from a patient sample (acute infection)

text: Germany

text: not provided

text: Homo sapiens

text: B6065, clone ST235 isolate

text: patient sample (acute infection) from Heidelberg, Germany

characteristic: isolation source

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa clnical isolate B6065


text: MHH

text: public

text: Pseudomonas aeruginosa clone ST235 strain MCF33, isolated from the airways of a cystic fibrosis patient (throat swab)

characteristic: description

text: Germany

text: not provided

characteristic: host health state

text: Homo sapiens

text: MCF33, clone ST235 isolate

text: cystic fibrosis airways sample from Munich, Germany

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa cystic fibrosis isolate MCF33

characteristic: title


text: MHH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Pseudomonas aeruginosa clone ST235 strain MCF108, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

text: MCF108, clone ST235 isolate

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa cystic fibrosis isolate MCF108


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MHH

text: public

text: Pseudomonas aeruginosa clone ST235 strain MCF244, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: MCF244, clone ST235 isolate

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa cystic fibrosis isolate MCF244


characteristic: ENA-LAST-UPDATE

text: MHH

characteristic: INSDC first public

text: public

text: Pseudomonas aeruginosa clone ST235 strain MCF639, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

text: MCF639, clone ST235 isolate

text: Pseudomonas aeruginosa F469

characteristic: organism

text: Pseudomonas aeruginosa F469

text: P. aeruginosa cystic fibrosis isolate MCF639


text: MHH

text: public

characteristic: Submitter Id

characteristic: collection date

text: Pseudomonas aeruginosa clone ST235 strain HCF400, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: HCF400, clone ST235 isolate

text: cystic fibrosis airways sample from Hannover, Germany

text: Pseudomonas aeruginosa F469

text: Pseudomonas aeruginosa F469

text: P. aeruginosa cystic fibrosis isolate HCF400


P. falciparum PfΔmei2 1

characteristic: External Id

characteristic: INSDC center name

text: public

text: P. falciparum PfΔmei2 1

tag: Namespace:KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

text: P. falciparum PfΔmei2 genome sequence


tag: attribute

text: MHH

text: public

text: Pseudomonas aeruginosa clone ST253 strain 110E8, isolated from a water sample (river)

characteristic: description

text: Germany

text: n. a.

text: 110E8, clone ST253 isolate

characteristic: isolate

text: water sample from Oker river, Schwuelper, Germany

characteristic: isolation source

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa environmental isolate 110E8


text: MHH

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Pseudomonas aeruginosa clone ST253 strain K4, isolated from a keratitis patient sample

text: United Kingdom

text: not provided

characteristic: host health state

text: Homo sapiens

text: K4, clone ST253 isolate

text: clnical sample (keratitis patient) from Bristol, UK

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa keratitis isolate K4

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MHH

text: public

characteristic: SRA accession

text: Pseudomonas aeruginosa clone ST253 strain K7, isolated from a keratitis patient sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: K7, clone ST253 isolate

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa keratitis isolate K7


characteristic: ENA-LAST-UPDATE

text: MHH

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Pseudomonas aeruginosa clone ST253 strain HCF202, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

text: HCF202, clone ST253 isolate

text: Pseudomonas aeruginosa D421

characteristic: organism

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate HCF202


characteristic: External Id

text: MHH

characteristic: INSDC center name

text: public

characteristic: collection date

text: Pseudomonas aeruginosa clone ST253 strain HCF209, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: HCF209, clone ST253 isolate

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate HCF209


text: MHH

text: public

text: Pseudomonas aeruginosa clone ST253 strain MCF228, isolated from the airways of a cystic fibrosis patient (throat swab)

characteristic: description

text: Germany

text: not provided

text: Homo sapiens

text: MCF228, clone ST253 isolate

characteristic: isolate

text: cystic fibrosis airways sample from Munich, Germany

characteristic: isolation source

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate MCF228


text: MHH

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Pseudomonas aeruginosa clone ST253 strain Zw61, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

characteristic: host health state

text: Homo sapiens

text: Zw61, clone ST253 isolate

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate Zw61


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MHH

text: public

text: Pseudomonas aeruginosa clone ST253 strain Zw86_2, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

text: Zw86_2, clone ST253 isolate

text: cystic fibrosis airways sample from Aberdeen, UK

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate Zw86_2

characteristic: title


characteristic: ENA-LAST-UPDATE

text: MHH

text: public

characteristic: SRA accession

text: Pseudomonas aeruginosa clone ST253 strain MCF37, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: MCF37, clone ST253 isolate

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate MCF37


text: MHH

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Pseudomonas aeruginosa clone ST253 strain SS8, isolated from the airways of a cystic fibrosis patient (throat swab)

text: Germany

text: not provided

text: Homo sapiens

text: SS8, clone ST253 isolate

text: cystic fibrosis airways sample from Lueneburg, Germany

text: Pseudomonas aeruginosa D421

characteristic: organism

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate SS8


characteristic: External Id

text: MHH

characteristic: INSDC center name

text: public

characteristic: collection date

text: Pseudomonas aeruginosa clone ST253 strain 012SA1, isolated from a water sample (river)

text: Germany

text: n. a.

text: 012SA1, clone ST253 isolate

text: water sample from Weser river, Hann. Muenden, Germany

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa environmental isolate 012SA1


text: MHH

text: public

text: Pseudomonas aeruginosa clone ST253 strain HCF212, isolated from the airways of a cystic fibrosis patient (throat swab)

characteristic: description

text: Germany

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: HCF212, clone ST253 isolate

characteristic: isolate

text: cystic fibrosis airways sample from Hannover, Germany

text: Pseudomonas aeruginosa D421

text: Pseudomonas aeruginosa D421

text: P. aeruginosa cystic fibrosis isolate HCF212


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 32213:c1ff0d60-e799-4a94-a49f-505670f7fc02

tag: Namespace:Max Planck Institute for Marine Microbiology

text: GFBIO

characteristic: broker name

text: SO245 (UltraPac GEOTRACES)

characteristic: campaign

text: 16s rRNA tag sequencing data from samples taken from surface waters (75m) during the SO245 UltraPac Cruise.

text: oceanic epipelagic zone biome [ENVO:01000035]

characteristic: environment (biome)

text: oceanic gyre [ENVO:01000074]

characteristic: environment (feature)

text: sea water [ENVO:00002149]

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: event label

text: Pacific Ocean

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

text: microbial community [PCO:1000004]

characteristic: organismal entity

text: Microbial community composition and polysaccharide processing potential in the South Pacific Gyre; G. Reintjes was benefited by the Max Planck Society; the UltraPac Expedition (SO245) was funded by the Deutsche Forschung Gemeinschaft (03G0245A), other funding from Horizon 2020 Research and Innovation program under the Marie Sklodowska-Curie grant agreement (840804)

characteristic: project name

text: Incubation

characteristic: sample collection device or method

characteristic: sample description

text: marine metagenome

text: Ion Torrent PGM

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Marine Microbiology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 32212:c1ff0d60-e799-4a94-a49f-505670f7fc02

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

text: SO245 (UltraPac GEOTRACES)

characteristic: campaign

characteristic: collection date

characteristic: description

text: oceanic gyre [ENVO:01000074]

text: sea water [ENVO:00002149]

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: marine metagenome

characteristic: organism

text: microbial community [PCO:1000004]

text: Incubation

text: marine metagenome

text: Ion Torrent PGM

text: true

characteristic: title

text: water


characteristic: ENA-CHECKLIST

text: public

text: 32211:c1ff0d60-e799-4a94-a49f-505670f7fc02

text: GFBIO

text: SO245 (UltraPac GEOTRACES)

characteristic: environment (biome)

text: oceanic gyre [ENVO:01000074]

characteristic: environment (feature)

text: sea water [ENVO:00002149]

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: event label

text: Pacific Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

text: microbial community [PCO:1000004]

characteristic: organismal entity

characteristic: project name

text: Incubation

characteristic: sample collection device or method

characteristic: sample description

text: marine metagenome

text: Ion Torrent PGM

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 32210:c1ff0d60-e799-4a94-a49f-505670f7fc02

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

text: SO245 (UltraPac GEOTRACES)

characteristic: campaign

characteristic: collection date

characteristic: description

text: oceanic gyre [ENVO:01000074]

text: sea water [ENVO:00002149]

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: marine metagenome

characteristic: organism

text: microbial community [PCO:1000004]

text: Incubation

text: marine metagenome

text: Ion Torrent PGM

text: true

characteristic: title

text: water