text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


status: PUBLIC

text: Pharyngula:Prim-5 ZFS:0000029 - Prim-15 ZFS:0000029

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCCAGTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCATTGAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGGCTCAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCAGATTC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACTAGTC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo heterozygous for kitlga, allele tc244b and wild type for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTCTATC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TATGTGGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single embryo heterozygous for kitlga, allele tc244b and wild type for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTACTCGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCGTTAGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo wildtype for kitlga, allele tc244b and heterozygous for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACCGAGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single embryo heterozygous for kitlga, allele tc244b and wild type for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTTCTCC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCGCACC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo heterozygous for kitlga, allele tc244b and wild type for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGCGTAC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 ZFS:0000029 - Prim-15 ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTACGAC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo wildtype for kitlga, allele tc244b and heterozygous for mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGACAGAC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

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 a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGAACAC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single embryo heterozygous for both kitlga, allele tc244b and mitfa, allele w2 from ZMP phenotype 155 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCATCCTA) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph155

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGGTTGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

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 a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Protruding-mouth - ZFS:0000035

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo obtained by crossing two fish heterozygous for dtb, allele 66ATUG plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGACTCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single wildtype sibling male E9.5 6 somite mouse embryo, with wildtype sibling parents derived from a Ddx51 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 6 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 6 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 7 somite mouse embryo, with wildtype sibling parents derived from a Ddx51 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 7 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single C57BL/6N wildtype mouse embryo forming part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 7 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 35 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus

characteristic: strain


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 35 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


characteristic: External Id

text: EBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single wildtype sibling male E9.5 36 somite mouse embryo, with wildtype sibling parents derived from a Ddx51 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 36 somite mouse embryo, with wildtype sibling parents derived from a Setd5 knockout line. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


E-MTAB-3424:hESC culture 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Massachusetts Institute of Technology

characteristic: INSDC center name

text: public

text: E-MTAB-3424:hESC culture 3

tag: Namespace:Massachusetts Institute of Technology

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: hESCs were differentiated to Stage 6 cells, INS+ cells comprised approximately 4% of all Stage 6 cells. A large proportion of INS+ cells also co-expressed the pancreatic hormone somatostatin, consistent with previous reports. Also see Hrvatin et al. 10.1073/pnas.1400709111 SI Experimental Procedures. Directed Differentiation. Processed sample was fixed with 4% paraformaldehyde, permabilized, antibody stained and mock sorted to collect all cells. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. The aim of this experiment was to test how well 4 different RNA-seq library construction techniques perform on partially degraded RNA.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture 3

type: has member


E-MTAB-3424:hESC culture 2

text: Massachusetts Institute of Technology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3424:hESC culture 2

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture 2

characteristic: title


E-MTAB-3424:hESC culture 1

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3424:hESC culture 1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: hESCs were differentiated to Stage 6 cells, INS+ cells comprised approximately 4% of all Stage 6 cells. A large proportion of INS+ cells also co-expressed the pancreatic hormone somatostatin, consistent with previous reports. Also see Hrvatin et al. 10.1073/pnas.1400709111 SI Experimental Procedures. Directed Differentiation. NA The aim of this experiment was to test how well 4 different RNA-seq library construction techniques perform on partially degraded RNA.

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: hESC culture 1


E-MTAB-3417:E18.5 pancreas islets

text: Massachusetts Institute of Technology

text: public

characteristic: SRA accession

text: E-MTAB-3417:E18.5 pancreas islets

text: ArrayExpress

text: house mouse

text: Protocols: Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: islet

characteristic: organism part

text: Mus musculus

text: Pdx1 minimal promoter-GFP on mixed/outbred background

characteristic: strain or line

text: E18.5 pancreas islets


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Harvard University

text: public

tag: Namespace:Harvard University

text: ArrayExpress

characteristic: cell cycle stage

text: HeLa

text: human

text: Protocols: HeLa cells were grown in standard DMEM media with sodium pyruvate (Gibco #11995073) with 10 % Bovine serum (Gibco #16170078), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240). HFF cells were grown in standard DMEM media with sodium pyruvate (Gibco #11995073) with 10 % FBS (BenchMark #100-101), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240). K562 cells were maintained in standard RPMI-1640 media with 2 mM L-glutamine (Gibco #22400-089) with 10% FBS (BenchMark #100-101), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240). To collect HeLs cells arrested in S-phase, cells were synchronized by double Thymidine block (2mM thymidine in grouth media). HeLa cells in G1 phase were obtained by double thymidine block followed by release into normal growth media for 12h (early G1) or 14h (middle G1). To collect mitotic cells, HeLa, HFF-1 and K562 cells were synchronized by double Thymidine block followed by release into normal growth media for several hous. Then cells were arrested in Metaphase by adding nocodazole at 100ng/mkl final concentration in grouth medai as described in (Naumova et al. 2013) Hi-C was performed following (Lieberman and van Berkum et al., Science, 2009) with modifications detailed in (Naumova et al., 2013).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: Harvard University

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: M

text: HeLa

characteristic: cell line

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Harvard University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-1948_2:CCHiC-HeLaS3CCL2p2-M-98percent

text: ArrayExpress

text: M

text: HeLa

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Harvard University

text: public

text: E-MTAB-1948_2:CCHiC-HeLaS3CCL2p2-G1-0.25FA

characteristic: Submitter Id

text: ArrayExpress

text: HeLa

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Harvard University

text: public

characteristic: SRA accession

text: E-MTAB-1948_2:CCHiC-HeLaS3CCL2p2-M-0.25FA

text: ArrayExpress

text: M

text: HeLa

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


status: KILLED

text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


E-MTAB-3429:Human islets rep 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Massachusetts Institute of Technology

characteristic: INSDC center name

text: public

text: E-MTAB-3429:Human islets rep 1

text: ArrayExpress

text: human

text: Protocols: Islets were dispersed to a single cell suspension using TrypLE Express (Invitrogen). Cells were passed through a 40 um filter (BD Falcon 352340) and washed with PBS at least twice. Cells were fixed and permeabilized with 4% PFA (Electron Microscopy Sciences), 0.1% saponin (Sigma-Aldrich 47036) in molecular grade PBS (Ambion) supplemented with 1:100 RNasin Plus RNase Inhibitor (Promega, N2615) for 30min at 4C. All the subsequent steps were carried out at 4C. Cells were pelleted by centrifugation at 3000g for 3min at 4C and washed in Wash Buffer: PBS containing 0.2% BSA (Gemini Bio-Products), 0.1% saponin (Sigma-Aldrich), 1:100 RNasin Plus RNase Inihibitor. Primary antibody staining was carried out while 3D rocking for 30min at 4C in Staining buffer containing PBS with 1% BSA, 0.1% saponin and 1:25 RNasin Plus RNase Inhibitor (note that certain antibodies may require longer incubation times). Cells were washed twice in Wash Buffer followed by secondary antibody staining in Staining buffer. Following secondary antibody staining cells were washed twice in Wash buffer and resuspended in Sort buffer containing PBS, 0.5% BSA, and 1:25 RNasin Plus RNase Inhibitor. Fixation, washing, staining and sorting were performed at a concentration of 5-10 M cells/ml. After sorting, cells were pelleted by centrifugation at 3000 g for 5' at 4 degrees C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50 degrees C and 15 minutes at 80 degrees C, we carried out the incubation for 3 hours at 50 degrees C. Cell lysates were frozen at -80 degrees C overnight before continuing the RNA isolation by the manufacturer's instructions. NA

text: Homo sapiens

text: Homo sapiens

text: islet

characteristic: organism part

text: Homo sapiens

text: Human islets rep 1


E-MTAB-3429:hESC culture 2

text: Massachusetts Institute of Technology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3429:hESC culture 2

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: hESCs were differentiated to Stage 6 cells, INS+ cells comprised approximately 4% of all Stage 6 cells. A large proportion of INS+ cells also co-expressed the pancreatic hormone somatostatin, consistent with previous reports. Also see Hrvatin et al. 10.1073/pnas.1400709111 SI Experimental Procedures. Directed Differentiation. Islets were dispersed to a single cell suspension using TrypLE Express (Invitrogen). Cells were passed through a 40 um filter (BD Falcon 352340) and washed with PBS at least twice. Cells were fixed and permeabilized with 4% PFA (Electron Microscopy Sciences), 0.1% saponin (Sigma-Aldrich 47036) in molecular grade PBS (Ambion) supplemented with 1:100 RNasin Plus RNase Inhibitor (Promega, N2615) for 30min at 4C. All the subsequent steps were carried out at 4C. Cells were pelleted by centrifugation at 3000g for 3min at 4C and washed in Wash Buffer: PBS containing 0.2% BSA (Gemini Bio-Products), 0.1% saponin (Sigma-Aldrich), 1:100 RNasin Plus RNase Inihibitor. Primary antibody staining was carried out while 3D rocking for 30min at 4C in Staining buffer containing PBS with 1% BSA, 0.1% saponin and 1:25 RNasin Plus RNase Inhibitor (note that certain antibodies may require longer incubation times). Cells were washed twice in Wash Buffer followed by secondary antibody staining in Staining buffer. Following secondary antibody staining cells were washed twice in Wash buffer and resuspended in Sort buffer containing PBS, 0.5% BSA, and 1:25 RNasin Plus RNase Inhibitor. Fixation, washing, staining and sorting were performed at a concentration of 5-10 M cells/ml. After sorting, cells were pelleted by centrifugation at 3000 g for 5' at 4 degrees C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50 degrees C and 15 minutes at 80 degrees C, we carried out the incubation for 3 hours at 50 degrees C. Cell lysates were frozen at -80 degrees C overnight before continuing the RNA isolation by the manufacturer's instructions. NA

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture 2


E-MTAB-3429:hESC culture 3

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3429:hESC culture 3

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: hESC culture 3

characteristic: title


E-MTAB-3429:Human islets rep 2

characteristic: ENA-CHECKLIST

text: Massachusetts Institute of Technology

text: public

characteristic: SRA accession

text: E-MTAB-3429:Human islets rep 2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: islet

text: Homo sapiens

text: Human islets rep 2


E-MTAB-3429:hESC culture 1

characteristic: ENA-FIRST-PUBLIC

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3429:hESC culture 1

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture 1


E-MTAB-3429:hESC culture 4

characteristic: ENA-LAST-UPDATE

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3429:hESC culture 4

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture 4


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: The University of Manchester

characteristic: INSDC center name

text: public

tag: Namespace:The University of Manchester

text: ArrayExpress

text: baker's yeast

text: Protocols: Grown in SCD-His media at 30oC to exponential phase (OD600 0.5-0.7), pelleted by centrifugation and snap frozen into liquid nitrogen. Samples lysed in Buffer A using a 6870 Freezer Mill (Spex). Lysates cleared by centrifuging twice at 15000 g. Nucleic acids extracted using Trizol Reagent. The aqueous phase was mixed with 70% ethanol and the RNA was purified using RNeasy Minikit (Qiagen). rRNA was depleted from samples using RibominusTM Eukaryote Kit for RNA-Seq (Invitrogen). Depleted samples were precipitated with 2.5x volumes ethanol, 1/10th volume 3M sodium acetate and 1μl glycogen, washed twice with 70% ethanol and re-suspended in 10 μl DEPC water. Sequencing libraries were generated using the whole Transcriptome Library preparation protocol provided with the SOLiD® Total RNA-Seq Kit.

text: MATa his3-∆1 leu2∆0 met15∆0 ura3∆0 PUF3::TAP-HIS3+

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: The University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Grown in SCD-His media at 30oC to exponential phase (OD600 0.5-0.7), pelleted by centrifugation and snap frozen into liquid nitrogen. Samples lysed in Buffer A using a 6870 Freezer Mill (Spex). Lysates cleared by centrifuging twice at 15000 g. Nucleic acids extracted using Trizol Reagent. The aqueous phase was mixed with 70% ethanol and the RNA was purified using RNeasy Minikit (Qiagen). Beads were pre-washed thrice with Buffer A and then added to 4mg/ml of lysate. Puf3p-TAGged samples were immunoprecipitated for 20 minutes at 4oC and washed five times with Buffer A containing 10 units/ml RNAsin, changing tubes twice during the washes and the final two washes were performed for 15 minutes each. After the final wash the beads were resuspended in 250 µl Buffer A and treated with Trizol. The aqueous phase was mixed with 70% ethanol and the RNA was purified using RNeasy Minikit (Qiagen). rRNA was depleted from samples using RibominusTM Eukaryote Kit for RNA-Seq (Invitrogen). Depleted samples were precipitated with 2.5x volumes ethanol, 1/10th volume 3M sodium acetate and 1μl glycogen, washed twice with 70% ethanol and re-suspended in 10 μl DEPC water. Sequencing libraries were generated using the whole Transcriptome Library preparation protocol provided with the SOLiD® Total RNA-Seq Kit

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen


E-MTAB-3427:Sample 30

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 30

tag: Namespace:Univeristy of Liverpool,

characteristic: Submitter Id

text: old

characteristic: age

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: mesenchymal stem cell

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: MSCs purchased from young and old donors grown in osteocenic media for 21 days grown in pellet culture in chondrogenic media grown as 3D tendonconstructs in tenogenic media miRNAeasy columns for RNA purification following Trizol treatment New England BioLabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to manufacturer’s instructions

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 30


E-MTAB-3427:Sample 18

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of Liverpool,

text: public

characteristic: SRA accession

text: E-MTAB-3427:Sample 18

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Protocols: MSCs purchased from young and old donors grown in osteocenic media for 21 days grown in pellet culture in chondrogenic media miRNAeasy columns for RNA purification following Trizol treatment New England BioLabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to manufacturer’s instructions

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 18

characteristic: title


E-MTAB-3427:Sample 16

text: Univeristy of Liverpool,

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3427:Sample 16

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Protocols: MSCs purchased from young and old donors grown in osteocenic media for 21 days grown as 3D tendonconstructs in tenogenic media miRNAeasy columns for RNA purification following Trizol treatment New England BioLabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to manufacturer’s instructions

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 16


E-MTAB-3427:Sample 6

text: Univeristy of Liverpool,

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3427:Sample 6

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

text: Protocols: MSCs purchased from young and old donors grown in pellet culture in chondrogenic media grown as 3D tendonconstructs in tenogenic media miRNAeasy columns for RNA purification following Trizol treatment New England BioLabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to manufacturer’s instructions

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 6


E-MTAB-3427:Sample 29

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 29

characteristic: Submitter Id

text: old

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 29


E-MTAB-3427:Sample 26

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 26

text: young

characteristic: age

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 26


E-MTAB-3427:Sample 3

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 3

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

characteristic: clinical information

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3


E-MTAB-3427:Sample 2

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 2

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-3427:Sample 21

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 21

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 21


E-MTAB-3427:Sample 24

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 24

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 24


E-MTAB-3427:Sample 1

text: Univeristy of Liverpool,

text: public

characteristic: SRA accession

text: E-MTAB-3427:Sample 1

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 1

characteristic: title


E-MTAB-3427:Sample 19

text: Univeristy of Liverpool,

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3427:Sample 19

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 19


E-MTAB-3427:Sample 27

text: Univeristy of Liverpool,

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3427:Sample 27

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 27


E-MTAB-3427:Sample 10

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 10

characteristic: Submitter Id

text: young

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

text: chondrogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 10


E-MTAB-3427:Sample 4

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 4

text: young

characteristic: age

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: osteogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 4


E-MTAB-3427:Sample 13

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 13

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: chondrogenic

characteristic: clinical information

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 13


E-MTAB-3427:Sample 22

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 22

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 22


E-MTAB-3427:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 5

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 5


E-MTAB-3427:Sample 28

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 28

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 28


E-MTAB-3427:Sample 23

text: Univeristy of Liverpool,

text: public

characteristic: SRA accession

text: E-MTAB-3427:Sample 23

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 23

characteristic: title


E-MTAB-3427:Sample 7

text: Univeristy of Liverpool,

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3427:Sample 7

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 7


E-MTAB-3427:Sample 8

text: Univeristy of Liverpool,

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3427:Sample 8

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: osteogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 8


E-MTAB-3427:Sample 11

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 11

characteristic: Submitter Id

text: young

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

text: chondrogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 11


E-MTAB-3427:Sample 9

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 9

text: young

characteristic: age

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 9


E-MTAB-3427:Sample 17

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 17

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

characteristic: clinical information

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 17


E-MTAB-3427:Sample 20

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 20

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: tendongenic

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 20


E-MTAB-3427:Sample 31

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 31

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 31


E-MTAB-3427:Sample 25

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of Liverpool,

text: public

text: E-MTAB-3427:Sample 25

text: young

text: ArrayExpress

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Protocols: MSCs purchased from young and old donors grown in osteocenic media for 21 days grown in pellet culture in chondrogenic media grown as 3D tendonconstructs in tenogenic media miRNAeasy columns for RNA purification following Trizol treatment

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 25


E-MTAB-3427:Sample 14

text: Univeristy of Liverpool,

text: public

characteristic: SRA accession

text: E-MTAB-3427:Sample 14

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: chondrogenic

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 14

characteristic: title


E-MTAB-3427:Sample 32

text: Univeristy of Liverpool,

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3427:Sample 32

text: old

text: ArrayExpress

text: mesenchymal stem cell

text: mesenchymal stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 32


text: University of Manchester

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University of Manchester

text: ArrayExpress

text: house mouse

text: Protocols: In this experiment two mouse lines (WT and Bmal1 knockout) were studied for circadian gene expression at four time points in a 24 hour period. All animal studies were performed in accordance with the 1986 UK Home Office Animal Procedures Act. Approval was provided by the local ethics committee. Mice were maintained at 20-22oC, with standard rodent chow available ad libitum and under 12:12 hr light dark schedule. Bmal1flox/flox mice were crossed onto a PER2::luc background. The PER2::luc mice carry the firefly luciferase gene fused in-frame with the 3’ end of the Per2 gene, creating a fusion protein reporter. Bmal1flox/flox - PER2::luc mice were subsequently crossed with Col2a1cre mice expressing cre recombinase under the control of the Col2a1 promoter20 to generate cartilage specific Bmal1 knock-out. All mice were bred in-house at the University of Manchester. Hip cartilage was obtained from 8-10 weeks old mice by dislocating the joint and peeling off the cartilage from the head of the femur using a scalpel blade. The tissue was immediately snap frozen in liquid nitrogen, and then stored at -80oC until mRNA extraction. Tissue was homogenised using a Mikro-Dismembrator S (Satorius Stedim Biotech) with the barrel and ball of the dismembrator pre-cooled in liquid nitrogen. mRNA was extracted using RNeasy micro kit (Qiagen) according to the manufacturer’s protocol. Illumina TruSeq Stranded mRNA Library Prep Kit

text: BMAL1 knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: hip cartilage

characteristic: organism part

text: Mus musculus

text: 05:00 AM

characteristic: time


text: University of Manchester

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 05:00 AM


text: University of Manchester

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 09:00 AM


characteristic: ENA-CHECKLIST

text: University of Manchester

text: public

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 05:00 PM


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Manchester

text: public

text: ArrayExpress

text: house mouse

text: BMAL1 knockout

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 05:00 PM


characteristic: External Id

text: University of Manchester

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: BMAL1 knockout

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 09:00 AM


text: University of Manchester

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 09:00 PM

characteristic: title


text: University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: BMAL1 knockout

text: Mus musculus

text: Mus musculus

text: hip cartilage

text: Mus musculus

text: 09:00 PM


text: The University of Manchester

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: Protocols: Grown in SCD-His media at 30oC to exponential phase (OD600 0.5-0.7), pelleted by centrifugation and snap frozen into liquid nitrogen. Samples lysed in Lola lysis buffer using a 6870 Freezer Mill (Spex). Lysates cleared by centrifugating twice at 15000 g. Nucleic acids extracted using Trizol Reagent. rRNA was depleted from samples using RibominusTM Eukaryote Kit for RNA-Seq (Invitrogen). Depleted samples were precipitated with 2.5x volumes ethanol, 1/10th volume 3M sodium acetate and 1μl glycogen, washed twice with 70% ethanol and re-suspended in 10 μl DEPC water. Sequencing libraries were generated using the whole Transcriptome Library preparation protocol provided with the SOLiD® Total RNA-Seq Kit.

text: Mat a; his3 1; leu2 0; met15 0; ura3 0; YLL013c::kanMX4

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum


E-MTAB-3432:Human islets

characteristic: ENA-CHECKLIST

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3432:Human islets

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80C for a later digestion. If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 10e7 nuclei. Volumes should be scaled as per cell number. Digestion buffer (850 ul per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 ul per 10e7 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 ug/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37C. DNaseI enzyme was combined with warmed digestion buffer for a final volume of 100 ul per 107 nuclei. If multiple concentrations of DNaseI were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37C. Pre- warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2ug/mL and samples were incubated overnight at 55C. DNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20C for 5-6 hours or at -80C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer. To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the 150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control). NA

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: islet

characteristic: organism part

text: Homo sapiens

text: Human islets


E-MTAB-3432:hESC culture

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Massachusetts Institute of Technology

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-3432:hESC culture

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: See Hrvatin et al. 10.1073/pnas.1400709111. Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80C for a later digestion. If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 10e7 nuclei. Volumes should be scaled as per cell number. Digestion buffer (850 ul per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 ul per 10e7 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 ug/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37C. DNaseI enzyme was combined with warmed digestion buffer for a final volume of 100 ul per 107 nuclei. If multiple concentrations of DNaseI were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37C. Pre- warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2ug/mL and samples were incubated overnight at 55C. DNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20C for 5-6 hours or at -80C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer. To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the 150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control). NA

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hESC culture


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Bioforsk - Norwegian Institute of Agricultural and Environmental Research

text: potato

text: Solanum tuberosum

text: Solanum tuberosum

characteristic: title


text: Bioforsk - Norwegian Institute of Agricultural and Environmental Research

text: public

characteristic: Submitter Id

text: potato

text: Solanum tuberosum

text: Solanum tuberosum


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: EBI

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Sample Test 150315


text: ES Cells

characteristic: ArrayExpress-CellType

text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: gRNA PCR

characteristic: sample description

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Total RNA

text: Mus musculus

characteristic: strain


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: earclip

characteristic: ArrayExpress-OrganismPart

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: genomic DNA from earclips

text: Mus musculus


text: embryo

text: earclip

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: genomic DNA from earclips

text: Mus musculus


text: embryo

text: earclip

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: genomic DNA from blastocyst

characteristic: sample description

text: Mus musculus


text: adult

text: earclip

text: mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: genomic DNA from earclips

text: Mus musculus


text: adult

text: earclip

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: DNA from blastocyst

text: Mus musculus


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: earclip

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: DNA from blastocyst

text: Mus musculus

characteristic: strain


text: Plasmodium vivax

text: SC

characteristic: INSDC first public

text: public

text: malaria parasite P. vivax

text: Plasmodium vivax

text: Plasmodium vivax


text: Normal

characteristic: ArrayExpress-Phenotype

text: Homo sapiens

text: SC

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Sigmoid Brush

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: Homo sapiens

text: Sigmoid Lavage

text: Homo sapiens


text: Normal

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: human

text: Homo sapiens

text: Sigmoid Biopsy

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: TI Brush

text: Homo sapiens


text: Normal

text: Homo sapiens

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Rectum Brush

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Rectum biopsey

characteristic: sample description

text: Homo sapiens


text: Normal

text: Homo sapiens

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: Rectum Lavage

text: Homo sapiens


text: Normal

text: Homo sapiens

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: TI Biopsy

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: TI Lavage

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Rectum Biopsy

text: Homo sapiens


text: Normal

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: SigmoidBiopsy

text: Homo sapiens


text: University College Dublin

text: public

tag: Namespace:University College Dublin

characteristic: block

text: ArrayExpress

characteristic: broker name

text: cattle

text: Protocols: 2 study groups. natural and experimentally infected miRneasy based extraction TruSeq Small RNA Sample Preparation Kit (Illumina)

characteristic: description

text: Johne's disease

characteristic: disease

characteristic: individual

text: naturally infected by Mycobacterium avium subspecies paratuberculosis

characteristic: infection

text: Bos taurus

text: Bos taurus

text: blood serum

characteristic: organism part

text: Bos taurus

text: female

characteristic: sex

text: frozen (-20 degree C) for approximately 10-15 years

characteristic: specimen with known storage state

text: 49 month

characteristic: time

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University College Dublin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: cattle

characteristic: common name

text: Johne's disease

text: Bos taurus

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 6 month


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College Dublin

characteristic: INSDC center name

text: public

characteristic: block

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: description

text: Johne's disease

text: experimentally infected (control) by Mycobacterium Avium subspecies paratuberculosis

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 0 month


text: University College Dublin

text: public

text: ArrayExpress

text: cattle

text: Johne's disease

characteristic: disease

characteristic: individual

characteristic: infection

text: Bos taurus

text: Bos taurus

text: blood serum

characteristic: organism part

text: Bos taurus

text: female

characteristic: sex

characteristic: specimen with known storage state

text: 43 month

characteristic: time


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University College Dublin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: cattle

text: Johne's disease

text: Bos taurus

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 43 month

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College Dublin

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: block

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

text: Johne's disease

text: Bos taurus

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 0 month


text: University College Dublin

text: public

text: ArrayExpress

text: cattle

characteristic: description

text: Johne's disease

characteristic: disease

characteristic: individual

characteristic: infection

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood serum

characteristic: organism part

text: Bos taurus

text: female

characteristic: sex

text: 49 month


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University College Dublin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: cattle

text: Johne's disease

text: Bos taurus

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

characteristic: specimen with known storage state

text: 6 month

characteristic: time


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College Dublin

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: block

text: ArrayExpress

text: cattle

text: Johne's disease

text: Bos taurus

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 46 month

characteristic: title


text: University College Dublin

text: public

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: Johne's disease

characteristic: disease

characteristic: individual

characteristic: infection

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood serum

text: Bos taurus

text: female

text: 46 month


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: DNA libraries made by the addition of tailed oligos in a second round of PCR.

characteristic: sample description

text: Danio rerio


text: Pharyngula:Prim-5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 190 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph190

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim-5 - ZFS:0000029

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 a single phenotypically normal embryo from ZMP phenotype 190 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TCCTCAAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph190

text: Danio rerio

text: mixed


text: Hatching:Long-pec - ZFS:0000033

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: ZMP_phenotype_188_1_phenotypic_2-sc-2249794

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for dmd, allele ta222a, from ZMP phenotype 188 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCCTGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph188

text: Danio rerio

text: mixed


characteristic: ENA-FIRST-PUBLIC

text: GSC

characteristic: INSDC first public

text: public

text: southern root-knot nematode

text: Meloidogyne incognita

text: Meloidogyne incognita


text: Segmentation:1-4 somites - ZFS:0000023

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 a single genotyped homozygous mutant embryo for tfap2a, allele sa24445 from ZMP phenotype 162 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGGTGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph162

text: Danio rerio

text: mixed


text: Segmentation:1-4 somites - ZFS:0000023

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped heterozygous embryo for tfap2a, allele sa24445 from ZMP phenotype 162 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTGTGTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph162

characteristic: sample description

text: Danio rerio

text: mixed


text: GSC

text: public

text: root-knot nematode

text: Meloidogyne javanica

text: Meloidogyne javanica


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 190 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph190

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 190 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TGAACTGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph190

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 191 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph191

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 191 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph191

text: Danio rerio

text: mixed

characteristic: strain


text: Hatching:Long-pec - ZFS:0000033

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_188_1_phenotypic_6-sc-2249798

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for dmd, allele ta222a, from ZMP phenotype 188 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph188

text: Danio rerio

text: mixed


text: Hatching:Long-pec - ZFS:0000033

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: ZMP_phenotype_188_1_phenotypic_9-sc-2249801

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for dmd, allele ta222a, from ZMP phenotype 188 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph188

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 177 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph177

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

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 a single phenotypically abnormal embryo from ZMP phenotype 178 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph178

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 178 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph178

characteristic: sample description

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 178 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph178

text: Danio rerio

text: mixed