IgG PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: IgG PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


IgG PE18 (SOW, EON, BR2)

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: IgG PE18 (SOW, EON, BR2)

tag: Namespace:ETH ZURICH

characteristic: Submitter Id

text: thale cress

characteristic: common name

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6

characteristic: title

type: has member


IgG PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: IgG PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


IgG PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: IgG PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


IgG PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: IgG PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


IgG PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: IgG PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


IgG PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: IgG PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: K27ac PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: K27ac PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: K27ac PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: K27ac PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: K27ac PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: K27ac PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: K27ac PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27ac PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: K27ac PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: K27me3 PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: K27me3 PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: K27me3 PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: K27me3 PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: K27me3 PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: K27me3 PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: K27me3 PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K27me3 PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: K27me3 PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: K4me3 PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: K4me3 PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: K4me3 PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: K4me3 PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: K4me3 PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: K4me3 PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: K4me3 PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K4me3 PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: K4me3 PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: K9ac PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: K9ac PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: K9ac PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: K9ac PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: K9ac PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: K9ac PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: K9ac PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9ac PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: K9ac PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: K9me2 PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: K9me2 PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: K9me2 PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: K9me2 PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: K9me2 PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: K9me2 PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: K9me2 PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


K9me2 PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: K9me2 PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: S10p PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: S10p PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: S10p PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: S10p PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: S10p PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: S10p PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: S10p PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S10p PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: S10p PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE7 (SOW, EON, BR1)

text: ETH ZURICH

text: public

text: S28p PE7 (SOW, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE8 (SOW, EOD, BR1)

text: ETH ZURICH

text: public

text: S28p PE8 (SOW, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE18 (SOW, EON, BR2)

text: ETH ZURICH

text: public

text: S28p PE18 (SOW, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE19 (SOW, EOD, BR2)

text: ETH ZURICH

text: public

text: S28p PE19 (SOW, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE42 (SWD, EON, BR1)

text: ETH ZURICH

text: public

text: S28p PE42 (SWD, EON, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE43 (SWD, EOD, BR1)

text: ETH ZURICH

text: public

text: S28p PE43 (SWD, EOD, BR1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE74 (SWD, EON, BR2)

text: ETH ZURICH

text: public

text: S28p PE74 (SWD, EON, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


S28p PE75 (SWD, EOD, BR2)

text: ETH ZURICH

text: public

text: S28p PE75 (SWD, EOD, BR2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis Leaf 6


text: UNIVERSITY OF GENEVA

text: public

tag: Namespace:UNIVERSITY OF GENEVA

text: Oocyst

characteristic: dev stage

text: Goussia janae

text: Goussia janae

text: Gjanae Transcriptome


text: UNIVERSITY OF EDINBURGH

text: public

tag: Namespace:UNIVERSITY OF EDINBURGH

text: Ronan Kapetanovic

characteristic: collected by

text: pig

text: Macrophage RNA-Seq libraries. Alveolar macrophages (AM) or bone marrow-derived macrophages (BMDM) in two conditions i.e. control (CTRL) or LPS-treated (LPS).

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: AM/CTRL

characteristic: tissue type

text: Macrophage RNA-Seq library


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF EDINBURGH

text: public

text: Ronan Kapetanovic

text: pig

text: Sus scrofa

text: Sus scrofa

text: AM/LPS

text: Macrophage RNA-Seq library


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF EDINBURGH

text: public

text: Ronan Kapetanovic

text: pig

text: Sus scrofa

text: Sus scrofa

text: BMDM/CTRL

text: Macrophage RNA-Seq library


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF EDINBURGH

text: public

text: Ronan Kapetanovic

text: pig

text: Sus scrofa

text: Sus scrofa

text: BMDM/LPS

text: Macrophage RNA-Seq library


characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

text: public

tag: Namespace:UNIVERSITY OF COPENHAGEN

text: human

text: UGANDA

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens

text: UGD


text: UNIVERSITY OF EDINBURGH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Dario Beraldi

text: pig

text: Pig CAGE library from alveolar macrophages

text: Sus scrofa

text: Sus scrofa

text: Alveolar macrophages

text: Pig CAGE library


text: UNIVERSITY OF WATERLOO

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF WATERLOO

text: insect gut metagenome

characteristic: sample date

characteristic: sample id

characteristic: sample well

text: insect gut metagenome

text: lab colony

characteristic: source

text: lab

text: 16S rRNA gene sequences from mosquito gut, sample id: 1

text: lab colony

characteristic: trt

characteristic: tub


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: description

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: lab colony

text: lab

text: 16S rRNA gene sequences from mosquito gut, sample id: 2

characteristic: title

text: lab colony


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

text: public

text: Pupae

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: Pupae

text: 16S rRNA gene sequences from mosquito gut, sample id: 3

text: High


text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Pupae

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: Pupae

text: 16S rRNA gene sequences from mosquito gut, sample id: 5

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: INSDC status

text: Adults

text: insect gut metagenome

characteristic: sample date

characteristic: sample id

text: insect gut metagenome

text: Field

text: Adults

text: 16S rRNA gene sequences from mosquito gut, sample id: 6

text: High


text: UNIVERSITY OF WATERLOO

text: public

text: Adults

text: insect gut metagenome

characteristic: sample well

text: insect gut metagenome

text: Field

characteristic: source

text: Adults

text: 16S rRNA gene sequences from mosquito gut, sample id: 7

text: High

characteristic: trt


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Adults

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: Adults

text: 16S rRNA gene sequences from mosquito gut, sample id: 8

text: Control

characteristic: tub


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: Adults

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Field

text: Adults

text: 16S rRNA gene sequences from mosquito gut, sample id: 9

characteristic: title

text: Control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF WATERLOO

text: public

text: Adults

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: Adults

text: 16S rRNA gene sequences from mosquito gut, sample id: 10

text: High


characteristic: External Id

text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 12

text: High


text: UNIVERSITY OF WATERLOO

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: insect gut metagenome

characteristic: sample date

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 13

text: Control


text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

characteristic: sample id

characteristic: sample well

text: insect gut metagenome

text: Field

characteristic: source

text: 16S rRNA gene sequences from mosquito gut, sample id: 14

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 15

text: Control

characteristic: trt


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 16

text: Control

characteristic: tub


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 17

characteristic: title

text: High


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 19

text: High


text: UNIVERSITY OF WATERLOO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 20

text: High


text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

characteristic: sample date

characteristic: sample id

characteristic: sample well

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 21

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: insect gut metagenome

text: insect gut metagenome

text: Field

characteristic: source

text: 16S rRNA gene sequences from mosquito gut, sample id: 22

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 23

text: Control

characteristic: trt


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 24

text: Control

characteristic: tub


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 25

characteristic: title

text: High


text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 26

text: High


text: UNIVERSITY OF WATERLOO

text: public

characteristic: INSDC status

text: insect gut metagenome

characteristic: sample date

characteristic: sample id

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 27

text: High


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: insect gut metagenome

characteristic: sample well

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 29

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Field

characteristic: source

text: 16S rRNA gene sequences from mosquito gut, sample id: 30

text: Control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 31

text: High

characteristic: trt


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 32

text: High

characteristic: tub


text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 33

characteristic: title

text: High


text: UNIVERSITY OF WATERLOO

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: insect gut metagenome

characteristic: sample date

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 34

text: High


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: insect gut metagenome

characteristic: sample id

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 35

text: Control


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: insect gut metagenome

characteristic: organism

characteristic: sample well

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 36

text: Control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

characteristic: source

text: 16S rRNA gene sequences from mosquito gut, sample id: 37

text: Control


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 38

text: Control

characteristic: trt


text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 39

text: High

characteristic: tub


text: UNIVERSITY OF WATERLOO

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 40

characteristic: title

text: Low


text: UNIVERSITY OF WATERLOO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: insect gut metagenome

characteristic: sample date

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 41

text: Low


text: UNIVERSITY OF WATERLOO

text: public

characteristic: description

text: insect gut metagenome

characteristic: organism

characteristic: sample id

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 42

text: Low


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

characteristic: sample well

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 43

text: Low


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

characteristic: source

text: 16S rRNA gene sequences from mosquito gut, sample id: 44

text: Low


text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: insect gut metagenome

text: insect gut metagenome

text: Field

text: 16S rRNA gene sequences from mosquito gut, sample id: 45

text: Low

characteristic: trt


text: INSTITUT PASTEUR

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:INSTITUT PASTEUR

text: Chromosome and plasmide sequences of VAP LM33 strain

text: France

characteristic: geographic location (country and/or sea)

text: Escherichia coli

text: Escherichia coli

characteristic: serovar

characteristic: strain

text: VAP LM33


Single colony_2 1

text: STELLENBOSCH UNIVERSITY

text: public

characteristic: SRA accession

text: Single colony_2 1

tag: Namespace:STELLENBOSCH UNIVERSITY

characteristic: Submitter Id

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Single colonies selected from rif mono clinical isolates

characteristic: title


Single colony_2 2

characteristic: ENA-CHECKLIST

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 2

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis


Single colony_2 3

characteristic: ENA-FIRST-PUBLIC

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 3

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 4

characteristic: ENA-LAST-UPDATE

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 4

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 5

characteristic: External Id

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 5

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 6

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 6

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 7

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 7

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 8

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 8

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 9

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 9

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Single colony_2 10

text: STELLENBOSCH UNIVERSITY

text: public

text: Single colony_2 10

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


Mimivirus montadette2

text: URMITE

text: public

text: Mimivirus montadette2

text: a defense system in Mimivirus confers resistance to virophage

characteristic: description

text: Mimivirus montadette2

text: Mimivirus montadette2

text: MIMIVIRE


Moumouvirus istres

text: URMITE

characteristic: INSDC center name

text: public

text: Moumouvirus istres

text: Moumouvirus istres

text: Moumouvirus istres

text: MIMIVIRE


Megavirus sete2

text: URMITE

characteristic: INSDC first public

text: public

text: Megavirus sete2

text: Megavirus sete2

text: Megavirus sete2

text: MIMIVIRE


Megavirus terrain_en_construction

text: URMITE

text: public

text: Megavirus terrain_en_construction

text: Megavirus terrain_en_construction

text: Megavirus terrain_en_construction

text: MIMIVIRE


Megavirus balcon

text: URMITE

text: public

text: Megavirus balcon

text: Megavirus balcon

text: Megavirus balcon

text: MIMIVIRE


Megavirus potager

text: URMITE

text: public

text: Megavirus potager

text: A defense system in Mimivirus confers resistance to virophage

text: Megavirus potager

text: Megavirus potager

text: MIMIVIRE


Megavirus feuillage

text: URMITE

text: public

text: Megavirus feuillage

text: Megavirus feuillage

text: Megavirus feuillage

text: MIMIVIRE


text: Estacion Experimental del Zaidin (CSIC)

text: public

tag: Namespace:Estacion Experimental del Zaidin (CSIC)

text: ArrayExpress

characteristic: broker name

text: Protocols: The strains were grown on LB plates for 48 hours and resuspended in 3 ml of 10 mM MgCl2. Ten ml of MMR minimal medium (Robertsen et al., 1982) were inoculated and the OD adjusted to an OD660 of 0.05. The strains were grown in MMR minimal medium at 20o C to an OD660=1.5. At OD660=1.5 in MMR liquid minimal medium, the cells were harvested, washed with sarkosyl 0.1% and cell pellets were immediately frozen in liquid nitrogen and conserved at -80oC until RNA isolation. rRNA removal with Ribo zero magnetic kit was performed by Macrogen. The cells were processed for RNA isolation using TRI Reagent®LS (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer instructions, except that the TRI Reagent was preheated at 70oC and the lysis step was carried out at 65oC. The RNA obtained was treated with RNase-free DNase I (Quiagen) followed by purification with RNeasy mini kit (Quiagen).RNA concentration was determined spectrophotometrically and its integrity was assessed by agarose gel electrophoresis. cDNA libraries were constructed by Macrogen.

text: fleQ mutant

characteristic: genotype

text: liquid medium

characteristic: growth condition

text: Pseudomonas syringae pv. tomato str. DC3000


text: Estacion Experimental del Zaidin (CSIC)

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Protocols: The strains were grown on LB plates for 48 hours, resuspended in 10 mM MgCl2 and adjusted to an OD660 of 2.0. Two μl aliquots were inoculated in the centre of of PAG plates (0.5% protease peptone No. 3 (Difco 212693) and 0.2% glucose with 0.5% Difco Bacto-Agar) and incubated at 25°C for 24 hours (wild type) or 25 hours (mutant). Swarmer cells were resuspended in 5 ml MgCl2 10 mM and harvested, washed with sarkosyl 0.1% and cell pellets were immediately frozen in liquid nitrogen and conserved at -80oC until RNA isolation. rRNA removal with Ribo zero magnetic kit was performed by Macrogen. The cells were processed for RNA isolation using TRI Reagent®LS (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer instructions, except that the TRI Reagent was preheated at 70oC and the lysis step was carried out at 65oC. The RNA obtained was treated with RNase-free DNase I (Quiagen) followed by purification with RNeasy mini kit (Quiagen).RNA concentration was determined spectrophotometrically and its integrity was assessed by agarose gel electrophoresis. cDNA libraries were constructed by Macrogen.

text: fleQ mutant

text: swarming plates


text: Estacion Experimental del Zaidin (CSIC)

text: public

text: ArrayExpress

text: wild type genotype

text: liquid medium


text: Estacion Experimental del Zaidin (CSIC)

text: public

text: ArrayExpress

text: wild type genotype

text: swarming plates


text: public

tag: Namespace:EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)

text: ArrayExpress

text: Protocols: Cells were grown in modified Hayflick medium miRNeasy kit from Qiagen (in column DNase) Strandâspecific RNA-seq library, the TruSeq Stranded mRNA Sample Prep Kit v2 (Illumina)

text: wild type genotype

text: 6 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)

text: public

text: ArrayExpress

text: wild type genotype

text: 6 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: wild type genotype

text: 96 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: 6 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: 96 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: 24 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: MPN027 knockin by transposon insertion

text: 24 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: MPN114 knockin by transposon insertion

text: 24 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: MPN397 knockin by transposon insertion

text: 6 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: MPN566 knockin by transposon insertion

text: 24 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: wild type genotype

text: 24 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: University of Dundee

text: public

tag: Namespace:University of Dundee

text: SASA

characteristic: bio material

text: 300 bp paired end MiSeq sequencing of a 315 bp amplicon from G. pallida mitochondrial Cytochrome B sequence amplified from approx 1000 samples each with unique barcode pair appended to primers.

text: Globodera pallida

text: Globodera pallida


text: public

characteristic: SRA accession

text: ArrayExpress

text: 7 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

characteristic: Submitter Id

text: ArrayExpress

text: 6 hours growth

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: ZMBH

text: public

text: ArrayExpress

text: Lister 427_pHD1313 pA+

characteristic: cell line

text: Protocols: log phase culture standard Illumina kit on 300nt fragments

text: cell suspension culture

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei

characteristic: title


characteristic: ENA-CHECKLIST

text: ZMBH

text: public

text: ArrayExpress

text: Tbr729 pA+

text: Protocols: rat buffy coat standard Illumina kit on 300nt fragments

text: rat buffy coat

text: Trypanosoma brucei

characteristic: organism

text: Trypanosoma brucei

text: Trypanosoma brucei


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ZMBH

text: public

text: ArrayExpress

text: LW024 pA+_1

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


characteristic: External Id

text: ZMBH

text: public

text: ArrayExpress

text: LW024 pA+_2

characteristic: description

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: LW032 pA+_1

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

text: public

text: ArrayExpress

characteristic: broker name

text: LW032 pA+_2

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

text: public

text: ArrayExpress

text: LW041 pA+_1

text: rat buffy coat

characteristic: growth condition

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

characteristic: INSDC last update

text: public

text: ArrayExpress

text: LW041 pA+_2

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

text: public

characteristic: INSDC status

text: ArrayExpress

text: LW031 pA+_1

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

text: public

text: ArrayExpress

text: LW031 pA+_2

text: rat buffy coat

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: ZMBH

text: public

text: ArrayExpress

text: Lister 427_procyclics pA+

text: cell suspension culture

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


E-MTAB-3792:Sample 4

text: public

text: E-MTAB-3792:Sample 4

tag: Namespace:Telethon Institute of Genetics and Medicine, TIGEM

characteristic: age

text: ArrayExpress

text: Non visually impaired donor

characteristic: clinical history

text: human

characteristic: common name

text: Protocols: In collaboration with the Fondazione Banca degli Occhi del Veneto (FBOV), we collected retina samples from 18 different donors. in compliance with the tenets of the Declaration of Helsinki and after obtaining the informed consent from the donorâs next of kin. The average post-mortem time of the 16 samples was 22 hours 40 min (ranging from 6 to 26 hours). Briefly, an incision was performed on the sclera and the scleral tissue was cut and removed leaving the rest of the eye bulb intact. The RPE/choroid was then removed as an intact sheet, revealing the neural retina. The latter was gently pulled away from the underlying vitreous body that remained intact. The dissected retinal tissue was visually inspected to exclude any cross contamination with the pigmented RPE/choroid and was immediately submerged in RNA Stabilisation Reagent (RNA later; Qiagen) to stabilise RNA and preserve gene expression profiles. More details in Parekh, M. et al. A simplified technique for in situ excision of cornea and evisceration of retinal tissue from human ocular globe. Journal of visualized experiments : JoVE, e3765, doi:10.3791/3765 (2012). mirneasy QIAGEN TruSeq Small RNA library preparation (Illumina)

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

text: Sample 4


E-MTAB-3792:Sample 5

characteristic: ENA-CHECKLIST

text: Telethon Institute of Genetics and Medicine, TIGEM

text: public

characteristic: SRA accession

text: E-MTAB-3792:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: Non visually impaired donor

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: retina

text: Homo sapiens

text: male

text: frozen specimen

text: Sample 5

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG

text: ArrayExpress

text: Protocols: Cross-linked chromatin was digested with DNase I Cells were grown in modified Hayflick medium DNAseq

characteristic: description

text: wild type genotype

characteristic: genotype

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: wild type genotype

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: Protocols: Cells were grown in modified Hayflick medium Chromatin Affinity purification with IgG DNAseq

text: RNA polymerase

characteristic: immunoprecipitate

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: Protocols: Cells were grown in modified Hayflick medium One sample was treated with Novobiocin 100 ug/ml Chromatin Affinity purification with IgG DNAseq

text: RNA polymerase

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: UNIVERSITY OF GENEVA

text: public

text: Goussia janae

text: Goussia janae

text: Left reads of Paired end transcriptome of G.janae


text: public

tag: Namespace:Whitney Laboratory for Marine Bioscience

text: common brandling worm

characteristic: common name

text: This is from the same library as the sample named Parent1

text: Eisenia fetida

text: Eisenia fetida


characteristic: ENA-CHECKLIST

text: Whitney Laboratory for Marine Bioscience

text: public

text: common brandling worm

text: This is from the same library as the sample named Parent2

text: Eisenia fetida

text: Eisenia fetida


text: public

characteristic: SRA accession

text: common brandling worm

text: Eisenia fetida

text: Eisenia fetida

text: Eisenia fetida genome


text: public

tag: Namespace:THE FEDERAL RESEARCH CENTER INSTITUTE OF CYTOLOGY AND GENETICS  The Siberian Branch of the Russian Academy of Sciences

characteristic: Submitter Id

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Rat tame 1


text: THE FEDERAL RESEARCH CENTER INSTITUTE OF CYTOLOGY AND GENETICS The Siberian Branch of the Russian Academy of Sciences

text: public

text: Norway rat

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: Rat tame 2


text: public

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Rat aggressive 1

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: public

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Rat aggressive 2


characteristic: ENA-LAST-UPDATE

text: John Innes Centre

text: public

tag: Namespace:John Innes Centre

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; wildtype

characteristic: ecotype

text: Triticum aestivum

text: Triticum aestivum


characteristic: External Id

text: John Innes Centre

characteristic: INSDC center name

text: public

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E4

text: Triticum aestivum

text: Triticum aestivum


text: John Innes Centre

text: public

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E5

characteristic: description

text: Triticum aestivum

text: Triticum aestivum


text: John Innes Centre

characteristic: INSDC first public

text: public

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E6

text: Triticum aestivum

text: Triticum aestivum


text: John Innes Centre

characteristic: INSDC last update

text: public

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E7

text: Triticum aestivum

text: Triticum aestivum


text: John Innes Centre

text: public

characteristic: INSDC status

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E8

text: Triticum aestivum

text: Triticum aestivum


text: John Innes Centre

text: public

text: bread wheat

text: Triticum aestivum carrying the Sr33 resistance gene; susceptible mutant E9

text: Triticum aestivum

text: Triticum aestivum


text: PHE

text: public

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae

characteristic: year isolated


text: PHE

text: public

text: Brainfrontallobe

characteristic: isolation site

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae


text: PHE

text: public

text: Sputum

text: Mycoplasma pneumoniae

text: Mycoplasma pneumoniae


Cryptosporidium hominis UdeA013

text: UDEA

text: public

text: Cryptosporidium hominis UdeA013

text: Colombia

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host

text: Feces

characteristic: isolation source

text: Cryptosporidium hominis

text: Cryptosporidium hominis

text: Whole genome shotgun sequencing of a human-derived isolate of C. hominis


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

tag: Namespace:Department of Internal Medicine 5 - Hematology/Oncology

characteristic: Submitter Id

text: human

characteristic: common name

characteristic: donor

text: Homo sapiens

text: Homo sapiens

text: sample

text: DNwo

characteristic: treatment


tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Internal Medicine 5 - Hematology/Oncology

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: sample

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Homo sapiens

text: sample

text: DNwo


Argentine Ants

text: public

text: Argentine Ants

tag: Namespace:Institute of Environmental Science & Research

text: Argentine ant

text: A pool of 60 Argentine ants from two nests, collected from Wellington, New Zealand

characteristic: description

text: Linepithema humile

text: Linepithema humile

text: Argentine Ant


Light

text: JIC

text: public

text: Light

text: Photosynthetic growth - ambient illumination, low nutrient

text: Euglena gracilis

text: Euglena gracilis

text: Euglena gracilis culture sample


Dark

text: JIC

text: public

text: Dark

text: Heterotrophic growth - no light source, high nutrient media culture

text: Euglena gracilis

text: Euglena gracilis

text: Euglena gracilis culture sample


text: European Molecular Biology Laboratory

text: public

tag: Namespace:European Molecular Biology Laboratory

text: 2 to 5h

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 10 ul of the final 1ml mix of any of the samples, just prior to antibody addition, equivalent of 1%, was put aside in a 1.5 ml tube at 4 degrees. For each input sample, 25 ul (always use the same amount used for the IP in process) of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, PAS were added to input samples and processed identically as IP-ed samples. Briefly, input samples were washed with 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 5 to 7

characteristic: developmental stage

text: egg laying

characteristic: initial time point

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

characteristic: sex

text: white eye mutation line, w[-]

characteristic: strain


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 5 to 7h

text: ArrayExpress

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L10_Mef2-DRE5-14-17h-IP-32-10

text: 14 to 17h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. Between 30 and 70 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Mef2 (DRE5 or DRC4) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 20 or 25 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 20 or 25 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 13 to 14

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: 7 to 10h

text: ArrayExpress

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

characteristic: organism

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: title


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 5 to 7h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. â30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Tin (EJRI) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 20 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 20 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted.â ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

text: 5 to 7h

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Twi (DNOH or DNOA) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 25 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 25 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

characteristic: description

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L12_Mef2-DRE5-10-14h-IP-54-9

text: 10 to 14h

text: ArrayExpress

text: stage 12 to 13

characteristic: developmental stage

text: egg laying

characteristic: initial time point

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

characteristic: sex

text: white eye mutation line, w[-]


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: 2 to 5h

text: ArrayExpress

text: stage 5 to 7

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

characteristic: Submitter Id

text: 7 to 10h

text: ArrayExpress

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: E-MTAB-3798:L13_Dvir_Bin-EHUD-7-10h-IP-68-4

text: 7 to 10h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Bin (EHUD) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 15 or 20 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 15 or 20 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

characteristic: organism

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3798:L13_Dvir_Mef2-DRC4-5-7h-IP-65-7

text: 5 to 7h

text: ArrayExpress

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: title


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: E-MTAB-3798:L13_Dvir_Mef2-DRC4-7-10h-IP-62-5

text: 7 to 10h

characteristic: age

text: ArrayExpress

characteristic: broker name

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L13_Dvir_Mef2-DRE5-2-5h-IP-66-7

text: 2 to 5h

text: ArrayExpress

characteristic: description

text: stage 5 to 7

characteristic: developmental stage

text: egg laying

characteristic: initial time point

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: E-MTAB-3798:L13_Dvir_Mef2-DRE5-5-7h-IP-61-13

text: 5 to 7h

text: ArrayExpress

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

characteristic: sex

text: white eye mutation line, w[-]


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L13_Dvir_Tin-EJRI-2-5h-IP-19-10

text: 2 to 5h

text: ArrayExpress

text: stage 5 to 7

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: strain


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: E-MTAB-3798:L13_Dvir_Twi-DNOA-7-10h-IP-68-9

characteristic: Submitter Id

text: 7 to 10h

text: ArrayExpress

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3798:L14_Dvir_Bin-EHUD-10-14h-IP-69-3

text: 10 to 14h

text: ArrayExpress

text: stage 12 to 13

text: egg laying

text: Drosophila virilis

characteristic: organism

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: E-MTAB-3798:L14_Dvir_Input-10-14h-IP-13-3

text: 10 to 14h

characteristic: age

text: ArrayExpress

text: stage 12 to 13

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: title


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L14_Dvir_Input-10-14h-IP-13-9

text: 10 to 14h

text: ArrayExpress

characteristic: broker name

characteristic: description

text: stage 12 to 13

characteristic: developmental stage

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: E-MTAB-3798:L14_Dvir_Input-14-17h-IP-32-12

text: 14 to 17h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 10 ul of the final 1ml mix of any of the samples, just prior to antibody addition, equivalent of 1%, was put aside in a 1.5 ml tube at 4 degrees. For each input sample, 25 ul (always use the same amount used for the IP in process) of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, PAS were added to input samples and processed identically as IP-ed samples. Briefly, input samples were washed with 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 13 to 14

text: egg laying

characteristic: initial time point

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L14_Dvir_Input-14-17h-IP-38-6

text: 14 to 17h

text: ArrayExpress

text: stage 13 to 14

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

characteristic: sex

text: white eye mutation line, w[-]


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: 2 to 5h

text: ArrayExpress

text: stage 5 to 7

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: strain


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3798:L14_Dvir_Input-5-7h-IP-39-12

characteristic: Submitter Id

text: 5 to 7h

text: ArrayExpress

text: stage 8 to 9

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: E-MTAB-3798:L14_Dvir_Input-7-10h-IP-43-3

text: 7 to 10h

characteristic: age

text: ArrayExpress

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

characteristic: organism

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L14_Dvir_Input-7-10h-IP-55-12

text: 7 to 10h

text: ArrayExpress

characteristic: broker name

characteristic: description

text: stage 10 to 11

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: title


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: E-MTAB-3798:L14_Dvir_Twi-DNOA-5-7h-IP-11-1

text: 5 to 7h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Twi (DNOH or DNOA) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 25 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 25 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 8 to 9

characteristic: developmental stage

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L15_Dvir_Bap-EJSJ-7-10h-IP-75-7

text: 7 to 10h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Bap (EJSJ) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 15 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 15 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 10 to 11

text: egg laying

characteristic: initial time point

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: E-MTAB-3797:poolB_DNase_13_1_14_X_dvir1417_30U

text: 14 to 17

unit: hour

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-micrometer Sefar Nitex membrane. The total number of nuclei was estimated by microscopy. DNase treatments were based closely on PMID: 23821440. Briefly, nuclei were permeabilised for 30min at 4C in PBS with 0.1% Triton-X and 0.02% NP40Nuclei were spun down at 2000G and resuspended in R-buffer [7.5mM Tris pH8, 45mM NaCl, 30mM KCl, 6mM MgCl2, 1mM CaCl2). Nuclei [~20x10e6 per digest] were then digested in 500uL R-buffer at 37C for 3min in a range of concentrations of DNase enzyme (10, 20, 30 or 50 units). After three minutes, the reaction was stopped with 500uL Stop-buffer [50mM Tris, pH-8, 100mM NaCL, 0.1% SDS, 100mM EDTA pH-8]. Reactions were then heated at 55C for 2 hours with 25uL of ProteinaseK [25mg/mL] and 300microg of RNaseA. An additional 25uL of ProK was then added and the reaction incubated over night at 65C. Following this step, digested DNA was isolated using Qiagen isolation kits and run out on a 1% agarose gel to assess digestion levels (as in PMID: 23821440). Optimal digests were then fractionated using sucrose gradients as in PMID: 23821440 to generate 330uL fractions. Fracitons 2 and 3 were then pooled and tested for quality using qPCR for known control regions of open chromatin. The digests with the highest qPCR enrichment were selected for library preparation. 'Illumina libraries were prepared according to manufacturers recommendations with small modifications. In short, 3-10ng of RNase treated, and reverse cross-linked DNA from our DNase protocol was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Modified versions of the Illumina PE adapters containing sample-specific molecular barcodes were ligated, after which the material was size selected with a mean of ~300 bp (size equals sheered chromatin fragments plus adapters) using AMPure beads. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 16 cycles according to manufacturer''s recommendation using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified using AMPure beads.'

text: stage 13 to 14

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

characteristic: sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3798:L15_Dvir_Bin-EHUD-10-14h-IP-74-11

text: 10 to 14h

text: ArrayExpress

text: Protocols: Wildtype Drosophila virilis (white eye mutation line) flies were grown in population cages at 25 degr. Staged populations of embryos were collected and aged at 25 degrees till the required stage of development is reached. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 485ul of 37% Formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collections was set aside to stage each collection. 30 ug of chromatin was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF, 1ul Leupeptin/Pepstain and 1 ul Aprotinin). For precipitation, 3ul Dvir-anti Bin (EHUD) antibody was added to each aliquot and incubated overnight at 4 degres on a rotating shaker. For each precipitation, 15 or 20 ul of 50% Protein A Sepharose (PAS) suspension were washed once with 1mL RIPA buffer + 1mg/ml BSA for blocking. In the morning, The antibody/antigen complexes were precipitated with 15 or 20 ul protein A sepharose at 4 degres for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with increase NaCl (500 mM), 1x in 250mM LiCl / 10mM Tris-HCl pH 8,0 / 1mM EDTA / 0,5% NP-40 / 0,5% sodium deoxycholate and 2x in TE. The DNA was eluted after protease digest and RNAase treatment by incubation at 65 degr overnight and phenol chloroform extracted. ~1g of embryos of early time points (or ~0.5 from later time points) were thawn quickly and resuspended in 15ml ice-cold PBS/Triton + protease inhibitors. Dounce homogenization 20x with loose pestle on ice followed by centrifugation at 400g for 1min at 4 degrees and transfer SN to fresh tube. Centrifuge SN at 1100g for 10 min at 4 degrees and discard SN. Resuspend pellet in 15 ml ice-cold Cell lysis buffer + protease inhibitor Dounce 20x with tight pestle on ice. Transfer two equal aliquots into 15 ml falcon tubes. Centrifuge at 2000g for 4min at 4 degrees to pellet the nuclei. Discard SN. Resuspend pellet in 1ml of ice-cold Nulear-Lysis Buffer + proteas inhibitor and incubate for 20 min at RT Add 1ml ice-cold Nuclear Lysis Buffer + proteas inhibitors Sonicate using Bioruptor in 15 ml faclon tubes with a max of 2 ml in them for 18 cycles with 30 seconds ON / 30 seconds OFF. Transfer to 1.5 ml tubes and centrifuge at 14000 rpm for 10 min at 4 degrees Take SN=chromatin and make aliquots of 400 ul and flash freeze in liquid nitrogen and store at -80 degrees. Cell lysis buffer: 5mM Hepes pH 8, 85mM KCl, 0.5% NP40 + protease inhibitors Nuclear lysis buffer: 50mM Hepes pH 8, 10mM EDTA Na2, 0.5% N-Laurylsarkosin + protease inhibitors Solexa libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of IP-purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters (in house) were ligated, after which the material was size selected at ~230-250 bp (size equals sheered chromatin fragments plus adapters) on a 2% GelGreen (Biotium) stained agarose gel using SafeXtractor-100 gel extractors (5Prime) under blue light. PCR amplification was performed using PE1.0 and PE2.0 primers (Illumina) for 14 cycles for Input samples and 16 cycles for IP-ed samples using the Phusion High-Fidelity PCR Kit (Finnzyme). The PCR-amplified library was purified on a 2% agarose gel, avoiding unincorporated primers and primer-self-ligation products. Library quality was assessed on a Bioanalyzer 2100 system (Agilent).

text: stage 12 to 13

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: strain


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: E-MTAB-3797:poolB_DNase_20_1_14_X_dvir1417_50U

characteristic: Submitter Id

text: 14 to 17

characteristic: age

text: ArrayExpress

text: stage 13 to 14

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3798:L15_Dvir_Bin-EHUD-14-17h-IP-74-21

text: 14 to 17h

text: ArrayExpress

characteristic: broker name

characteristic: description

text: stage 13 to 14

text: egg laying

text: Drosophila virilis

characteristic: organism

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: E-MTAB-3797:poolA_DNase_20_1_14_X_dvir25_30U

text: 2 to 5

text: ArrayExpress

text: stage 5 to 7

text: egg laying

text: Drosophila virilis

text: Drosophila virilis

text: Drosophila virilis

text: mixed sex

text: white eye mutation line, w[-]

characteristic: title