text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (CTTGTACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


status: PUBLIC

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TGGTTGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TCTCGGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TAAGCGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TCCGTCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TGTACCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TTCTGTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TCTGCTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TTGGAGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TCGAGCGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TGATACGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TGCATAGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at blastula - high stage (3.33 hpf). A 8 base indexing sequence (TTGACTCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (ATCACGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (CGATGTTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (TTAGGCAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (TGACCACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (ACAGTGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (GCCAATGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (CAGATCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (ACTTGATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (GATCAGCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at segmentation - 14-19 somites stage (16 hpf). A 8 base indexing sequence (TAGCTTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TGCGATCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TTCCTGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TAGTGACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TACAGGAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TCCTCAAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TGTGGTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TAGTCTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TTCCATTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TCGAAGTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TAACGCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TTGGTATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at pharyngula - prim 5 stage (24 hpf). A 8 base indexing sequence (TGAACTGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TGGTTGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TAAGCGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TCCGTCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TGTACCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TTCTGTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TCTGCTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TTGGAGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TCGAGCGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TGATACGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TGCATAGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at hatching - long pec stage (48 hpf). A 8 base indexing sequence (TTGACTCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TGCGATCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TTCCTGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TAGTGACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TACAGGAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TCCTCAAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TGTGGTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TAGTCTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TTCCATTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TCGAAGTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TAACGCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TTGGTATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - protruding mouth (72 hpf) stage. A 8 base indexing sequence (TGAACTGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TACTTCGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TCTCACGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TCAGGAGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TAAGTTCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TCCAGTCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TGTATGCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TCATTGAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TGGCTCAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TATGCCAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TCAGATTC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 4 (96 hpf stage. A 8 base indexing sequence (TTCAGCTC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TGTCTATC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TATGTGGC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TTACTCGC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TCGTTAGC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TACCGAGC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TGTTCTCC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TTCGCACC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TTGCGTAC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TCTACGAC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TGACAGAC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TAGAACAC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at larval - day 5 (120 hpf) stage. A 8 base indexing sequence (TCATCCTA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: public

tag: Namespace:Department of Biochemistry, University of Cambridge, UK

text: ArrayExpress

characteristic: broker name

text: fission yeast

characteristic: common name

text: Protocols: Cells were grown in yeast extract medium (Moreno et al., 1991, Methods Enzymol. 194, 795-823) at 32C, incubated for 5 minutes with 100 ug/ml cycloheximide, pelleted at 4C and frozen in liquid N2 RNA was extracted using a hot phenol extraction method as described in Lyne et al. (2003) BMC Genomics 4:27. Total RNA was fragmented by mixing 20 ul of RNA with 20 ul of 2X alkaline fragmentation buffer (2 mM EDTA, 100 mM Na2CO3) followed by incubation for 15 minutes at 95 degrees C. Samples were run on 15% TBE-urea gels (Life Technologies), and fragments of around 28 nucleotides were extracted from the gel. RNA samples were purified using Purelink RNA microcolumns (Life Technologies) as described by the manufacturer, except that the samples were initially passed through the column in the presence of 70% ethanol (to favour binding of small RNAs). Samples were then treated with poly nucleotide kinase (PNK, Fermentas) and polyadenylated using 12 units of poly-(A) polymerase (NEB) at 37C for 45 minutes. Reverse transcription reactions were performed using custom primers containing an anchored oligo(dT), 4 nucleotides of known sequence used for multiplexing, and 5 random nucleotides that serve as unique molecular identifiers. Reverse transcription products were gel-purified and circularised using CircLigase II (Epicentre), and amplified by PCR with custom library primers for 12 or 15 cycles.

characteristic: description

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: 968 h90

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Gorilla beringei

characteristic: ArrayExpress-Species

text: SC

text: public

text: eastern gorilla

text: Gorilla beringei

text: Gorilla beringei


text: Wildtype

characteristic: ArrayExpress-Genotype

text: Spleen

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-TimePoint

characteristic: ArrayExpress-Treatment

text: SC

text: public

text: house mouse

text: Mus musculus

text: DNA from cells

characteristic: sample description

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL6/N / C57BL6/N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TGCGATCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus

characteristic: strain


text: C57BL6/N / C57BL6/N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TTCCTGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


text: C57BL6/N / C57BL6/N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TAGTGACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL6/N / C57BL6/N

text: Whole embryo

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TACAGGAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Mus musculus


text: C57BL6/N / C57BL6/N

text: Whole embryo

text: male

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TCCTCAAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


text: C57BL6/N / C57BL6/N

text: Whole embryo

text: male

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TGTGGTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus

characteristic: strain


text: C57BL6/N / C57BL6/N

text: Whole embryo

text: female

text: Mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TAGTCTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


text: C57BL6/N / C57BL6/N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TTCCATTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL6/N / C57BL6/N

text: Whole embryo

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TCGAAGTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Mus musculus


text: C57BL6/N / C57BL6/N

text: Whole embryo

text: male

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from C57BL/6N embryos. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project. A 10 base indexing sequence (TAACGCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: The two parental haploid strains were grown overnight in 5 ml YPD (Yeast Extract 10 g/L, Bactopeptone 20 g/L, Dextrose 20 g/L). 100 microliter of each cell suspensions were plated on YPD agar. The cells were incubated at 30C for 24h to allow them to mate. The cell layer was then scraped from the plate and resuspended in 1 ml sterile water. 200 microliter of this suspension were plated on selective media to allow for the selection of diploid cells. This step was repeated three times per cross. The cells were grown for 48h at 30C. The mitochondrial DNA extraction protocol was adapted from Defontaine et al. (1991). The cells were scraped from the plates and resuspended in 1 ml water. They were harvested by centrifugation 3 min at 6000 rpm and washed once with 1 ml water. The cell pellet was washed once in 1ml water and once in 1ml Wash Buffer (1.2 M Sorbitol, 50 mM Tris pH 7.5, 50 mM EDTA, 2% beta-mercaptoethanol). The pellet was then resuspended in 1 ml Solution A (0.5 M Sorbitol, 50 mM Tris pH 7.5, 10 mM EDTA, 2% beta-mercaptoethanol), 100 U Zymolyase 100T (Amsbio) were added and the cells were incubated at 37C for 45 min under gentle horizontal shaking (400 rpm). The suspension was then centrifuged at 4000 rpm for 10 min. The supernatant was transferred to a new 1.5 ml tube and centrifuged at 14000 rpm for 15 min. The crude mitochondrial pellet was washed three times with 1 ml Solution A, resuspended in 400 microl Solution B (100 mM NaCl, 10 mM EDTA, 50 mM Tris pH 8) and incubated at room temperature for 30 min to allow for lysis. The mtDNA was then purified by phenol-chloroform extraction followed by ethanol precipitation. The mtDNA pellet was resuspended in 50 microl EB buffer (10 mM Tris pH 8). RNAs were degraded by RNAse cocktail treatment for 1h at 37C. The mitochondrial DNA libraries were generated using a protocol adapted from Wilkening et al. (2013). 3 to 10 micrograms of mitochondrial DNA were sheared using the S220 Focused-ultrasonicator (Covaris) with the following conditions: Duty cycle: 20%, Intensity: 5, Cycles/burst: 200, Duration: 45 sec, Temperature: 4C. The 350 bp fragments were purified using 1 volume Agencourt AMPure XP beads (Beckman Coulter). We performed end-repair, A-addition and adapter ligation on these fragments; heat inactivation of the enzymes was performed after each step. The samples were purified using 1 volume Agencourt AMPure XP beads and the libraries were amplified by PCR (98C for 45 sec, 12 cycles: (98C for 15 sec, 65C for 30 sec, 72C for 30 sec), 72C for 5 min). This step was performed using 2 to 10 ng of DNA, 2X Phusion High Fidelity PCR Master Mix (NEB) and 0.2 microM PE1.0 and PE2.0 primers (Illumina). The PCR products were then cleaned with 1 volume Agencourt AMPure XP beads and the yield was quantified with a Qubit Fluorometer (Life Technologies). Up to 13 samples were pooled and purified for 400-450 bp fragments on an E-gel (Life Technologies). The multiplexed libraries were sequenced on a Hiseq 2000, yielding between 2.8 and 42 million reads per sample

characteristic: description

text: MATa/MATalpha ura3delta/ura3delta lys53delta/LYS5 his3delta/HIS3

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Hybrid S288c SK1

characteristic: strain

characteristic: title


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: MATa/MATalpha hodelta/ho::hisG LYS2/lys2delta GAL2/gal2delta ura3delta/URA3 his3delta/HIS3 ntg1delta::KanMX-klURA3/ntg1delta::KanMX-klURA3

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Hybrid S288c YJM789


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: One colony of each parental haploid strains was grown overnight in 5 ml YPD (Yeast Extract 10 g/L, Bactopeptone 20 g/L, Dextrose 20 g/L). 100 microliter of each cell suspensions were plated on YPD agar. The cells were incubated at 30C for 24h. The mitochondrial DNA extraction protocol was adapted from Defontaine et al. (1991). The cells were scraped from the plates and resuspended in 1 ml water. They were harvested by centrifugation 3 min at 6000 rpm and washed once with 1 ml water. The cell pellet was washed once in 1ml water and once in 1ml Wash Buffer (1.2 M Sorbitol, 50 mM Tris pH 7.5, 50 mM EDTA, 2% beta-mercaptoethanol). The pellet was then resuspended in 1 ml Solution A (0.5 M Sorbitol, 50 mM Tris pH 7.5, 10 mM EDTA, 2% beta-mercaptoethanol), 100 U Zymolyase 100T (Amsbio) were added and the cells were incubated at 37C for 45 min under gentle horizontal shaking (400 rpm). The suspension was then centrifuged at 4000 rpm for 10 min. The supernatant was transferred to a new 1.5 ml tube and centrifuged at 14000 rpm for 15 min. The crude mitochondrial pellet was washed three times with 1 ml Solution A, resuspended in 400 microl Solution B (100 mM NaCl, 10 mM EDTA, 50 mM Tris pH 8) and incubated at room temperature for 30 min to allow for lysis. The mtDNA was then purified by phenol-chloroform extraction followed by ethanol precipitation. The mtDNA pellet was resuspended in 50 microl EB buffer (10 mM Tris pH 8). RNAs were degraded by RNAse cocktail treatment for 1h at 37C. The mitochondrial DNA libraries were generated using a protocol adapted from Wilkening et al. (2013). 3 to 10 micrograms of mitochondrial DNA were sheared using the S220 Focused-ultrasonicator (Covaris) with the following conditions: Duty cycle: 20%, Intensity: 5, Cycles/burst: 200, Duration: 45 sec, Temperature: 4C. The 350 bp fragments were purified using 1 volume Agencourt AMPure XP beads (Beckman Coulter). We performed end-repair, A-addition and adapter ligation on these fragments; heat inactivation of the enzymes was performed after each step. The samples were purified using 1 volume Agencourt AMPure XP beads and the libraries were amplified by PCR (98C for 45 sec, 12 cycles: (98C for 15 sec, 65C for 30 sec, 72C for 30 sec), 72C for 5 min). This step was performed using 2 to 10 ng of DNA, 2X Phusion High Fidelity PCR Master Mix (NEB) and 0.2 microM PE1.0 and PE2.0 primers (Illumina). The PCR products were then cleaned with 1 volume Agencourt AMPure XP beads and the yield was quantified with a Qubit Fluorometer (Life Technologies). Up to 13 samples were pooled and purified for 400-450 bp fragments on an E-gel (Life Technologies). The multiplexed libraries were sequenced on a Hiseq 2000, yielding between 2.8 and 42 million reads per sample

text: MATa ura3delta his3delta, MATalpha ho::hisG lys2delta gal2delta

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: S288c plus YJM789


characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: MATa ura3delta his3delta

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: ArrayExpress

text: baker's yeast

text: MATa ura3delta lys53delta

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: MATa/MATalpha hodelta/ho::hisG LYS2/lys2delta GAL2/gal2delta ura3delta/URA3 his3delta/HIS3 mhr1delta::KanMX-klURA3/mhr1delta::KanMX-klURA3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Hybrid S288c YJM789


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: MATa/MATalpha hodelta/ho::hisG LYS2/lys2delta GAL2/gal2delta ura3delta/URA3 his3delta/HIS3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Hybrid S288c YJM789


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: MATa/MATalpha hodelta/ho::hisG LYS2/lys2delta GAL2/gal2delta ura3delta/URA3 his3delta/HIS3 mgt1delta::KanMX-klURA3/mgt1delta::KanMX-klURA3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Hybrid S288c YJM789


characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: MATalpha ura3delta his3delta

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: MATalpha ho::hisG lys2delta gal2delta

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: public

tag: Namespace:European Molecular Biology Laboratory, Developmental Biology Unit

text: ArrayExpress

characteristic: broker name

text: B_domain-INV-M-ATT (inversion)

characteristic: chromosomal aberration

text: house mouse

text: Protocols: The whole embryos, latral and medial parts of forebrains, and heart were taken from E11.5d embryos. The limbs were taken from E12.5d embryos. The cells from the forebrains and the heart were dissociated by pipetting gently and passed through the Falcon Cell Strainers with 70um pore. Then they were fixed in 12 ml of 2% PFA/PBS at the room temperature for 10 min. 1.5 ml of 1 M glycine was added to quench the PFA. The cells were washed once in PBS and then frozen in Liquid nitrogen and stored at -80 degrees C. They were then incubated in 1 ml of the lysis buffer (50 mM Tris (pH7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, 1x complete proteinase inhibitors (Roche)) at 4 degrees C for 10 minutes. For the limbs and the whole embryo, instead, the single cell nuclei were prepared passing the fixed and lysed cells through needles for several times. After treating the nuclei in 0.3% SDS for 1 hour, followed by an additional 1 hour incubation with 2.5% Triton X-100, we digested the fixed genomic DNA with NlaIII enzyme at 37 degrees C for overnight. After the NlaIII was heat-inactivated, we ligated the DNA with T4 DNA ligase at 16 degrees C for overnight. Then the DNA was reverse cross-linked and purified through phenol-chloroform extraction and ethanol precipitation. The ligated DNA was then subjected to digestion by the second enzyme (DpnII) and ligation. After the ethanol precipitation, the eluted DNA was further purified twice with QIAquick PCR Purification Kit (QIAGEN). The concentration of the DNA was measured by NanoDrop. The inverse PCR was performed using 3.2ug of the libraries as templates except for the one from INV-M whole embryo, for which we used 1.8ug to obtain the 4C library.The reading primers had 3-6 nucleotides of tag sequence between the Illumina read adaptor and the annealing sequence, so that we could demultiplex the libraries after sequencing them together. The PCR products were purified with the High Pure PCR Product Purification Kit (Roche), and subsequently with QIAquick PCR Purification Kit (QIAGEN).

text: embrynoic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


text: European Molecular Biology Laboratory, Developmental Biology Unit

text: public

text: ArrayExpress

text: ap2c-wtHEART-CCGTA (wild type)

text: house mouse

characteristic: description

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: strain

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: A_domain-wt-CAT (wild type)

text: house mouse

characteristic: common name

text: embrynoic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Bmp7-wtHEART-CCAC (wild type)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Bmp7-INV-L2-CACTG (inversion)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


text: public

text: ArrayExpress

characteristic: broker name

text: Bmp7-del1-TCCG (deletion)

characteristic: chromosomal aberration

text: house mouse

text: embrynoic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


text: public

text: ArrayExpress

text: A_domain-INV-L2-GCTG (inversion)

text: house mouse

characteristic: description

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: strain

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: ArrayExpress

text: B_domain-wtHEART-TGGAG (wild type)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: ap2c-INV-L2-CAGG (inversion)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: ap2c-wtLFB-GCTA (wild type)

characteristic: chromosomal aberration

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: lateral forebrain

text: Mus musculus

text: fresh specimen


text: public

text: ArrayExpress

text: ap2c-wtMFB-GGAA (wild type)

text: house mouse

characteristic: description

text: embrynoic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: medial forebrain

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Bmp7-wtLFB-GCC (wild type)

text: house mouse

characteristic: common name

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: lateral forebrain

text: Mus musculus

text: fresh specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: ArrayExpress

text: A_domain-INV-M-ATGG (inversion)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

text: ArrayExpress

text: ap2c-del1-TGCCG (deletion)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: A_domain-wtHEART-TCTGAG (wild type)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: fresh specimen


text: public

text: ArrayExpress

characteristic: broker name

text: ap2c-wtE12Limb-TCG (wild type)

characteristic: chromosomal aberration

text: house mouse

characteristic: description

text: embrynoic day 12.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: limb bud

text: Mus musculus

text: fresh specimen


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Bmp7-INV-M-AGCG (inversion)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: ArrayExpress

text: ap2c-INV-M-AGCTAG (inversion)

text: house mouse

characteristic: common name

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Bmp7-wtMFB-TATA (wild type)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: medial forebrain

text: Mus musculus

text: fresh specimen


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: ap2c-wt-ATCGTG (wild type)

text: house mouse

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


text: public

text: ArrayExpress

characteristic: broker name

text: Bmp7-wtE12Limb-TGA (wild type)

characteristic: chromosomal aberration

text: house mouse

characteristic: description

text: embrynoic day 12.5

text: Mus musculus

text: Mus musculus

text: limb bud

characteristic: organism part

text: Mus musculus

text: fresh specimen


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Bmp7-wt-ATAG (wild type)

text: house mouse

text: embrynoic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: ArrayExpress

text: B_domain-wt-GGCC (wild type)

text: house mouse

characteristic: common name

text: embrynoic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: EMBL European Bioinformatics Institute

characteristic: INSDC center name

text: public

tag: Namespace:EMBL European Bioinformatics Institute

text: ArrayExpress

text: western wild mouse

text: Protocols: as described in Gonclaves et al. 2012. Extensive compensatory cis-trans regulation in the evoluition of mouse gene expression. Genome research. 22:2376-2384

text: Mus spretus

text: Mus spretus

text: liver

text: Mus spretus

text: SPRET/EiJ

characteristic: title


text: EMBL European Bioinformatics Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Ryukyu mouse

text: Mus caroli

characteristic: organism

text: Mus caroli

text: liver

text: Mus caroli

text: Caroli/EiJ


text: EMBL European Bioinformatics Institute

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: as described in Gonclaves et al. 2012. Extensive compensatory cis-trans regulation in the evoluition of mouse gene expression. Genome research. 22:2376-2384 mice were generated by the KO experiment performed as detailed in Kyrmizi et al 2006. Plasticity and expanding complexity of the hepatic transcription factor network during liver development. Genes & Development, 20: 2293-2305 as described in Gonclaves et al. 2012. Extensive compensatory cis-trans regulation in the evoluition of mouse gene expression. Genome research. 22:2376-2384 rna-seq library was prepared as described in Parkhomchuk D, Boradina T, Amstislavsky V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123. doi: 10.1093/nar/gkp596.

characteristic: description

text: gene knock-out

characteristic: genetic modification

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: EMBL European Bioinformatics Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus


characteristic: External Id

text: University of Manchester

text: public

tag: Namespace:University of Manchester

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Rex1GFPd2 mouse ES cells were maintained in NDiff N2B27 media in the presence of CHIR99021 and PD0325901 as described in Yang et al., 2012. For time series of differentiation, the media containing inhibitor was removed and replaced with NDiff N2B27 media as time indicated. ES cells were cross-linked as described in Lee et al., 2006. Yang SH, Kalkan T, Morrisroe C, Smith A, Sharrocks AD. (2012) PLoS Genet. 2012;8(12):e1003112. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. QIAGEN PCR extraction kit ChIP-seq was performed as described in Lee et al., 2006, with the following modifications. The crosslinked material was sheared by water bath sonication using biorupter, at high level, 30 secs on/ 30 secs off, 4 degrees C. Immunoprecipitation was performed by incubating 4x10^6 cells with 2 ug of Oct4 antibodies (N-19; Santa Cruz), overnight at 4 degrees C. Lee TI, Johnstone SE, Young RA. (2006) Nat Protoc. 1(2):729-48. Chromatin immunoprecipitation and microarray-based analysis of protein location.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: capzb1_hi1858bTg_clutch_1__mutant_1-sc-1923705

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (ATCACGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: capzb1_hi1858bTg_clutch_1__sibling_1-sc-1923706

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (CGATGTTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_2-sc-1923707

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTAGGCAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_2-sc-1923708

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGACCACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_3-sc-1923709

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (ACAGTGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_3-sc-1923710

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GCCAATGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_4-sc-1923711

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (CAGATCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_4-sc-1923712

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (ACTTGATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_5-sc-1923713

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GATCAGCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_5-sc-1923714

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAGCTTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_6-sc-1923715

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GGCTACAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_6-sc-1923716

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (CTTGTACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_7-sc-1923717

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGGTTGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_7-sc-1923718

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCTCGGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_8-sc-1923719

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAAGCGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_8-sc-1923720

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCCGTCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_9-sc-1923721

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGTACCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_9-sc-1923722

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTCTGTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_10-sc-1923723

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCTGCTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_10-sc-1923724

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTGGAGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_11-sc-1923725

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCGAGCGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_11-sc-1923726

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGATACGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__mutant_12-sc-1923727

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGCATAGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: capzb1_hi1858bTg_clutch_1__sibling_12-sc-1923728

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from capzb1, allele hi1858bTg clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTGACTCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_1-sc-1923729

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTCCTGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__mutant_2-sc-1923730

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAGTGACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_2-sc-1923731

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TACAGGAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__mutant_3-sc-1923732

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCCTCAAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_3-sc-1923733

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGTGGTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__mutant_4-sc-1923734

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAGTCTTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_4-sc-1923735

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTCCATTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__mutant_5-sc-1923736

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCGAAGTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_5-sc-1923737

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAACGCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__mutant_6-sc-1923738

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTGGTATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_1__sibling_6-sc-1923739

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGAACTGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_1-sc-1923740

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TACTTCGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_1-sc-1923741

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCTCACGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_2-sc-1923742

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCAGGAGG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_2-sc-1923743

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAAGTTCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_3-sc-1923744

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCCAGTCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_3-sc-1923745

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGTATGCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_4-sc-1923746

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCATTGAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_4-sc-1923747

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGGCTCAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_5-sc-1923748

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TATGCCAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_5-sc-1923749

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCAGATTC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_mutant_6-sc-1923750

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TACTAGTC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: gmds_p31erb_clutch_2_sibling_6-sc-1923751

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from gmds, allele p31erb clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTCAGCTC) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: The Pirbright Institute

text: public

tag: Namespace:The Pirbright Institute

text: 10 hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: African malaria mosquito

text: Protocols: The mosquitoes were kept in the insectary conditions at 27C, 80% RH, and 12h light/12h dark cycle. Larvae were reared in pans with de-ionized water and fed daily with ground fish food (Tetramin). Pans containing mature 4th instar larvae were inspected every hour, and newly pupated individuals transferred into marked pans with clean de-ionized water. Samples were collected at appropriate time intervals and sexed prior to grinding in TRIzol. The samples were ground in TRIzol and stored at -70C. Total RNA was isolated using PureLink RNA Mini Kit (Ambion) according to the manufacturer's protocol. RNA quality was evaluated using Qubit RNA assay (Life Technologies) and on a PerkinElmer GX using the HT RNA Reagent Kit (PerkinElmer) prior to construction of libraries. The libraries were constructed with the PerkinElmer Sciclone NGS Workstation using the TruSeq RNA protocol (Illumina Inc.). mRNA was isolated from 1 ug of total RNA by a poly-A+ pull down using biotin beads and fragmented. First strand cDNA was synthesised, followed by the second strand synthesis. The ends of the samples were repaired using the 3' to 5' exonuclease activity to remove the 3' overhangs, and the polymerase activity to fill in the 5' overhangs, creating blunt ends. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. This strategy ensured a low rate of chimera formation. The ligated products were subjected to a bead-based size selection using Beckman Coulter XP beads (Beckman Coulter). This removed the majority of un-ligated adapters, as well as any adapters that may have ligated to one another. Prior to hybridisation to the flow cell, the samples were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The PCR was performed with a PCR primer cocktail that annealed to the ends of the adapters. The insert size of the libraries was verified by running an aliquot of the DNA library on a PerkinElmer GX using the High Sensitivity DNA chip (PerkinElmer) and the concentration was determined by using a High Sensitivity Qubit assay (Life Technologies) and q-PCR. Prior to hybridisation to the flow cell, the samples were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The PCR was performed with a PCR primer cocktail that annealed to the ends of the adapter. The insert size of the libraries was verified by running an aliquot of the DNA library on a PerkinElmer GX using the High Sensitivity DNA chip (PerkinElmer) and the concentration was determined by using a High Sensitivity Qubit assay (Life Technologies) and q-PCR.

characteristic: description

text: pupae

characteristic: developmental stage

text: Pimperena

characteristic: genotype

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

text: Pimperena

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: The Pirbright Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 20 hour

text: ArrayExpress

text: African malaria mosquito

text: pupae

text: Pimperena

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

text: fresh specimen

text: Pimperena


characteristic: ENA-FIRST-PUBLIC

text: The Pirbright Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 20 hour

text: ArrayExpress

text: African malaria mosquito

text: pupae

text: Pimperena

text: Anopheles gambiae

characteristic: organism

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena

characteristic: strain


characteristic: External Id

text: The Pirbright Institute

text: public

text: 4 hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: African malaria mosquito

characteristic: common name

characteristic: description

text: pupae

text: Pimperena

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena


text: The Pirbright Institute

text: public

text: 4 hour

text: ArrayExpress

text: African malaria mosquito

text: pupae

characteristic: developmental stage

text: Pimperena

characteristic: genotype

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

text: Pimperena

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: The Pirbright Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 10 hour

text: ArrayExpress

text: African malaria mosquito

text: pupae

text: Pimperena

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena


characteristic: ENA-FIRST-PUBLIC

text: University of Oxford

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Oxford

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: ESCs were grown without feeders, on tissue culture dishes coated wth PBS+1% gelatine, in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% foetal calf serum (FCS, Seralab), 2 mM L-glutamine, 1x non-essential amino acids, 50 mM 2-mercaptoethanol, 50 ug/ml penicillin/streptomycin (Invitrogen) and LIF-conditioned medium, made in house, at a concentration equivalent to 1000 U/ml. (Reference: Nesterova, T. B., Popova, B. C., Cobb, B. S., Norton, S., Senner, C. E., Tang, Y. A., Spruce, T., Rodriguez, T. A., Sado, T., Merkenschlager, M. et al. (2008) 'Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a, Epigenetics Chromatin 1(1): 2.) 5 x 107 cells were fixed with 2 uM Ethylene glycol bis[succinimidylsuccinate] (ThermoScientific) for 1 h and then 1% formaldehyde for 15 min at RT. The reaction was quenched with glycine (0.125M) and nuclei prepared in LB1 (50 mM HEPES-KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA-NaOH pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1x complete EDTA-free protease inhibitors (Roche)). Nuclei were washed in LB2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA-NaOH pH 8.0, 0.5 mM EGTA and 1x complete EDTA-free protease inhibitors) and lysed in LB3 (10 mM Tris-HCl, pH 8, 100 mM NaCl, 1 mM EDTA-NaOH pH 8.0, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine and 1x complete EDTA-free protease inhibitors). Chromatin was sheared in a BioRuptor sonicator (Diagenode) to produce DNA fragments with a length of <1 kb. Triton X-100 was added (1% final) and cell debris cleared by centrifugation before the sample was diluted ten-fold with dilution buffer (1% Triton X-100, 2 mM EDTA-NaOH pH 8.0, 150 mM NaCl, 20 mM Tris-HCl pH 8.0 and 1x complete EDTA-free protease inhibitors). Samples were pre-cleared and incubated with antibodies overnight at 4C, after removal of input aliquots. Antibodies for ChIP-seq were H3K27me3 (Diagenode pAB -069-100), H3K36me3 (Abcam AB9050), anti-Suz12 (Cell Signalling 3737S), anti-Ring1B (Atsuta et al., 2001). Antibody complexes were collected with 30 ul BSA and tRNA blocked rProtein A Sepharose beads and were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA-NaOH pH 8.0, 150 mM NaCl, 20 mM Tris-Cl pH 8.0), high salt buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA-NaOH pH 8.0, 150 mM NaCl, 20 mM Tris-Cl pH 8.0), LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Na-Deoxycholate, 1 mM EDTA-NaOH pH 8.0, 10 mM TrisHCl pH 8.0) and twice with TE buffer. Complexes were eluted from beads by incubation with 100 ul Elution Buffer (1% SDS, 0.1 M NaHCO3) first at 65 degrees C for 5 min, and subsequently for 30 min with vortexing at 25C. NaCl was added to a final concentration of 200 mM and cross-links were reversed overnight at 65C. DNA was recovered after treatment with 100 ug/ml DNase-free RNase A at 42C for 90 min and Proteinase K (0.2mg/ml) for 1 h at 45C using ChIP DNA Clean & concentration columns (Zymo) and eluted in 10 ul volume. Undiluted purified DNA concentration was quantified using the PicoGreen dsDNA Quantitation Kit (Molecular Probes) and post-sonicated to <300 bp. Around 30 ng was sent to the Oxford Genomics Centre and 5 ng was used to prepare libraries using the NEBNext DNA Library Prep Master Mix Set for Illumina.

text: gene knock out

characteristic: genetic modification

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen


characteristic: External Id

text: University of Oxford

text: public

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: gene knock out

text: Dnmt1/Dnmt3a/Dnmt3b triple knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: strain


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:HUBRECHT INSTITUTE, UTRECHT, THE NETHERLANDS

text: human

text: TLA

text: Homo sapiens

text: Homo sapiens

text: TLA

characteristic: title


characteristic: ENA-LAST-UPDATE

text: HUBRECHT INSTITUTE, UTRECHT, THE NETHERLANDS

characteristic: INSDC center name

text: public

text: human

text: TLA

text: Homo sapiens

text: Homo sapiens

text: TLA


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: TLA

text: Mus musculus

text: Mus musculus

text: TLA


text: female

characteristic: ArrayExpress-Sex

text: Pan troglodytes

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: chimpanzee

text: Pan troglodytes

text: Pan troglodytes


text: male

text: Pan troglodytes

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: chimpanzee

text: Pan troglodytes

text: Pan troglodytes


characteristic: External Id

text: University of Toronto

text: public

tag: Namespace:University of Toronto

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: The HEK293_M2 + RHOXF2 stable cell line (PB-TGcMV-Neo) were seeded in 10cm-dishes, cultivated 24 hours in the presence or absence of doxycycline (2microgram/ml final) before been treated with 40nM of mitomycin C or DMSO (control) during a 2-days period. Total RNA was extracted (RNeasy Mini Kit - Qiagen), mRNA-focused libraries was generated from 1ug of total RNA (Illumina TruSeq RNA Sample Preparation Kit V.2). Cells were treated with 40nM of mitomycin C or DMSO (control) during a 2-days period. Total RNA was extracted (RNeasy Mini Kit Qiagen) mRNA-focused libraries was generated from 1ug of total RNA (Illumina TruSeq RNA Sample Preparation Kit V.2)

text: RHOXF2 not overexpressed in HEK293

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state