text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAACATT) 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_ph114

text: Danio rerio

text: mixed


status: PUBLIC

text: Larval:Day 12 - ZFS:0000039

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole larvae

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGTCGTGT) 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_ph114

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAATCTGT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

characteristic: ArrayExpress-DevelopmentalStage

text: Whole larvae

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 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTACATCT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCATGGCT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTAGCCT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCGCTAT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGAATGAT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGCCAAT) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTCCTTG) 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_ph114

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped homozygous mutant larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTAAGGTG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

characteristic: ArrayExpress-DevelopmentalStage

text: Whole larvae

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 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGGATGG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTGTCGG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGATTAGG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATAGAGG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped heterozygous larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAATCCG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GACCTTAG) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCCTGTTC) 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_ph114

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCACTGTC) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

characteristic: ArrayExpress-DevelopmentalStage

text: Whole larvae

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 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTAACTC) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

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 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATTCATC) 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_ph114

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larvae

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 12 dpf genotyped wild type larvae for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCTTGGC) 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_ph114

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

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 wild type zebrafish embryo collected at pharyngula - prim 5 stage (24 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool1-sc-2124874

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGACGGA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool2-sc-2124875

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTGAAGA) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool3-sc-2124876

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTCTTCA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool4-sc-2124877

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGTTCCA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool5-sc-2124878

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGAAGCCA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool6-sc-2124879

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACCACCA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_116_24hpf_pool7-sc-2124880

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCGTGAA) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ZMP_phenotype_116_24hpf_pool8-sc-2124881

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGTGAGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_116_24hpf_pool9-sc-2124882

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATCTCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool10-sc-2124883

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTGTCCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_116_24hpf_pool11-sc-2124884

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 5 stage (24 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GACGGATT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAACATT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGTCGTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAATCTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTACATCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCATGGCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTAGCCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCGCTAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGAATGAT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGCCAAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTCCTTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

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 wild type zebrafish embryo collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTAAGGTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool1-sc-2124897

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTGTCGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_117_30hpf_pool2-sc-2124898

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGATTAGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ZMP_phenotype_117_30hpf_pool3-sc-2124899

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATAGAGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_117_30hpf_pool4-sc-2124900

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) 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.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool5-sc-2124901

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAATCCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool6-sc-2124902

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GACCTTAG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool7-sc-2124903

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCCTGTTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool8-sc-2124904

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCACTGTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool9-sc-2124905

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTAACTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_117_30hpf_pool10-sc-2124906

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATTCATC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula:Prim 15 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_117_30hpf_pool11-sc-2124907

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of 8 wild type zebrafish embryos collected at pharyngula - prim 15 stage (30 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCTTGGC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


E-MTAB-2915:esgRNAi no2

text: public

text: E-MTAB-2915:esgRNAi no2

tag: Namespace:DKFZ/ZMBH Alliance, University of Heidelberg, Heidelberg, Germany

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: esgts > esgRNAi Protocols: esg-Gal4ts flies were crossed to either w1118 (esgtsCon), UASt-esg (UAS-esg) or esgRNAiJF03134 (esgRNAi) and shifted for 24 hours to 29 degrees C to induce transgene expression. 80-90 midguts were prepared for each genotype. For midgut cell dissociation for RNA-Seq, 1 mg/ml of Elastase were added per sample and guts incubated for 1 h at 27 degrees C, shaking at 600 rpm. To help dissociation, samples were pipetted vigorously every 15 min. For FACS profiling, tissue dissociation was performed by treatment with 7.5 mg/ml of Collagenase for 45 min followed by addition of 50 ul of 10X Trypsin/EDTA (Sigma) for 15-20 min. For RNA-Seq, a minimum of 20,000 GFP+ cells/condition was sorted on a FACS Aria II Flow Cytometer (BD Biosciences) using a 70 um nozzle and FACS Diva software. Intestinal cells obtained from w1118 animals where used to control for auto-fluorescence and set sorting gates. Dead cells were excluded from the sorting procedure by staining with 3 ul of Propidium Iodide (1 mg/ml, Life Technologies/Molecular Probes). RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Life Technologies). mRNA was amplified using the Arcturus RiboAmp HS Plus Amplification Kit (Life Technologies). Amplified RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

characteristic: description

text: esgRNAi knockdown

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgRNAi no2

characteristic: title

type: has member


E-MTAB-2915:C1 UAS-dIAP no1

characteristic: ENA-FIRST-PUBLIC

text: DKFZ/ZMBH Alliance, University of Heidelberg, Heidelberg, Germany

text: public

text: E-MTAB-2915:C1 UAS-dIAP no1

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: MyoIAts > UAS-dIAP Protocols: MyoIAts was used to drive transgene expression for 24 hours at 29 degrees C. 25 adult female intestines per genotype were dissected and midguts were homogenized in Trizol (Life Technologies). RNA was isolated by Phenol/Chloroform extraction, followed by purification of the RNA containing fractions using RNAeasy columns supplied with the RNAeasy Mini Kit (Qiagen). RNA was Poly-A-selected. RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: C1 UAS-dIAP no1


E-MTAB-2915:D1 Control no1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2915:D1 Control no1

text: ArrayExpress

text: fruit fly

text: MyoIAts > Empty vector RNAi VDRC60100 Protocols: MyoIAts was used to drive transgene expression for 24 hours at 29 degrees C. 25 adult female intestines per genotype were dissected and midguts were homogenized in Trizol (Life Technologies). RNA was isolated by Phenol/Chloroform extraction, followed by purification of the RNA containing fractions using RNAeasy columns supplied with the RNAeasy Mini Kit (Qiagen). RNA was Poly-A-selected. RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: MyoIAts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D1 Control no1


E-MTAB-2915:UAS-esg no4

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-2915:UAS-esg no4

text: ArrayExpress

text: fruit fly

text: esgts > UASt-esg Protocols: esg-Gal4ts flies were crossed to either w1118 (esgtsCon), UASt-esg (UAS-esg) or esgRNAiJF03134 (esgRNAi) and shifted for 24 hours to 29 degrees C to induce transgene expression. 80-90 midguts were prepared for each genotype. For midgut cell dissociation for RNA-Seq, 1 mg/ml of Elastase were added per sample and guts incubated for 1 h at 27 degrees C, shaking at 600 rpm. To help dissociation, samples were pipetted vigorously every 15 min. For FACS profiling, tissue dissociation was performed by treatment with 7.5 mg/ml of Collagenase for 45 min followed by addition of 50 ul of 10X Trypsin/EDTA (Sigma) for 15-20 min. For RNA-Seq, a minimum of 20,000 GFP+ cells/condition was sorted on a FACS Aria II Flow Cytometer (BD Biosciences) using a 70 um nozzle and FACS Diva software. Intestinal cells obtained from w1118 animals where used to control for auto-fluorescence and set sorting gates. Dead cells were excluded from the sorting procedure by staining with 3 ul of Propidium Iodide (1 mg/ml, Life Technologies/Molecular Probes). RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Life Technologies). mRNA was amplified using the Arcturus RiboAmp HS Plus Amplification Kit (Life Technologies). Amplified RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: UAS-esg no4


E-MTAB-2915:D3 Control no3

characteristic: External Id

text: public

text: E-MTAB-2915:D3 Control no3

text: ArrayExpress

text: fruit fly

text: MyoIAts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D3 Control no3


E-MTAB-2915:esgRNAi no3

characteristic: INSDC center name

text: public

text: E-MTAB-2915:esgRNAi no3

text: ArrayExpress

text: fruit fly

text: esgRNAi knockdown

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgRNAi no3


E-MTAB-2915:A1 UAS-esg no1

text: public

text: E-MTAB-2915:A1 UAS-esg no1

text: ArrayExpress

text: fruit fly

text: MyoIAts > UASt-esg Protocols: MyoIAts was used to drive transgene expression for 24 hours at 29 degrees C. 25 adult female intestines per genotype were dissected and midguts were homogenized in Trizol (Life Technologies). RNA was isolated by Phenol/Chloroform extraction, followed by purification of the RNA containing fractions using RNAeasy columns supplied with the RNAeasy Mini Kit (Qiagen). RNA was Poly-A-selected. RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: A1 UAS-esg no1


E-MTAB-2915:esgts control no2

text: public

text: E-MTAB-2915:esgts control no2

text: ArrayExpress

text: fruit fly

text: esgts crossed to w1118 Protocols: esg-Gal4ts flies were crossed to either w1118 (esgtsCon), UASt-esg (UAS-esg) or esgRNAiJF03134 (esgRNAi) and shifted for 24 hours to 29 degrees C to induce transgene expression. 80-90 midguts were prepared for each genotype. For midgut cell dissociation for RNA-Seq, 1 mg/ml of Elastase were added per sample and guts incubated for 1 h at 27 degrees C, shaking at 600 rpm. To help dissociation, samples were pipetted vigorously every 15 min. For FACS profiling, tissue dissociation was performed by treatment with 7.5 mg/ml of Collagenase for 45 min followed by addition of 50 ul of 10X Trypsin/EDTA (Sigma) for 15-20 min. For RNA-Seq, a minimum of 20,000 GFP+ cells/condition was sorted on a FACS Aria II Flow Cytometer (BD Biosciences) using a 70 um nozzle and FACS Diva software. Intestinal cells obtained from w1118 animals where used to control for auto-fluorescence and set sorting gates. Dead cells were excluded from the sorting procedure by staining with 3 ul of Propidium Iodide (1 mg/ml, Life Technologies/Molecular Probes). RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Life Technologies). mRNA was amplified using the Arcturus RiboAmp HS Plus Amplification Kit (Life Technologies). Amplified RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: esgts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgts control no2


E-MTAB-2915:A3 UAS-esg no3

text: public

text: E-MTAB-2915:A3 UAS-esg no3

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: A3 UAS-esg no3


E-MTAB-2915:A2 UAS-esg no2

text: public

text: E-MTAB-2915:A2 UAS-esg no2

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: A2 UAS-esg no2


E-MTAB-2915:C4 UAS-dIAP no4

text: public

text: E-MTAB-2915:C4 UAS-dIAP no4

text: ArrayExpress

text: fruit fly

text: UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: C4 UAS-dIAP no4


E-MTAB-2915:B4 UAS-esg+dIAP no4

text: public

text: E-MTAB-2915:B4 UAS-esg+dIAP no4

text: ArrayExpress

text: fruit fly

text: MyoIAts > UASt-esg+UAS-dIAP Protocols: MyoIAts was used to drive transgene expression for 24 hours at 29 degrees C. 25 adult female intestines per genotype were dissected and midguts were homogenized in Trizol (Life Technologies). RNA was isolated by Phenol/Chloroform extraction, followed by purification of the RNA containing fractions using RNAeasy columns supplied with the RNAeasy Mini Kit (Qiagen). RNA was Poly-A-selected. RNA integrity was determined with an Agilent 2100 Bioanalyzer before library generation. cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and NEBNext Multiplex Oligos for Illumina (NEB) were used for multiplexing.

text: UAS-esg+UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: B4 UAS-esg+dIAP no4


E-MTAB-2915:C3 UAS-dIAP no3

text: public

text: E-MTAB-2915:C3 UAS-dIAP no3

text: ArrayExpress

text: fruit fly

text: UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: C3 UAS-dIAP no3


E-MTAB-2915:D4 Control no4

text: public

text: E-MTAB-2915:D4 Control no4

text: ArrayExpress

text: fruit fly

text: MyoIAts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D4 Control no4


E-MTAB-2915:D2 Control no2

text: public

text: E-MTAB-2915:D2 Control no2

text: ArrayExpress

text: fruit fly

text: MyoIAts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D2 Control no2


E-MTAB-2915:A4 UAS-esg no4

text: public

text: E-MTAB-2915:A4 UAS-esg no4

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: A4 UAS-esg no4


E-MTAB-2915:B1 UAS-esg+dIAP no1

text: public

text: E-MTAB-2915:B1 UAS-esg+dIAP no1

text: ArrayExpress

text: fruit fly

text: UAS-esg+UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: B1 UAS-esg+dIAP no1


E-MTAB-2915:B2 UAS-esg+dIAP no2

text: public

text: E-MTAB-2915:B2 UAS-esg+dIAP no2

text: ArrayExpress

text: fruit fly

text: UAS-esg+UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: B2 UAS-esg+dIAP no2


E-MTAB-2915:UAS-esg no3

text: public

text: E-MTAB-2915:UAS-esg no3

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: UAS-esg no3


E-MTAB-2915:esgts control no4

text: public

text: E-MTAB-2915:esgts control no4

text: ArrayExpress

text: fruit fly

text: esgts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgts control no4


E-MTAB-2915:UAS-esg no6

text: public

text: E-MTAB-2915:UAS-esg no6

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: UAS-esg no6


E-MTAB-2915:esgRNAi no4

text: public

text: E-MTAB-2915:esgRNAi no4

text: ArrayExpress

text: fruit fly

text: esgRNAi knockdown

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgRNAi no4


E-MTAB-2915:B3 UAS-esg+dIAP no3

text: public

text: E-MTAB-2915:B3 UAS-esg+dIAP no3

text: ArrayExpress

text: fruit fly

text: UAS-esg+UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: B3 UAS-esg+dIAP no3


E-MTAB-2915:C2 UAS-dIAP no2

text: public

text: E-MTAB-2915:C2 UAS-dIAP no2

text: ArrayExpress

text: fruit fly

text: UAS-dIAP overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: C2 UAS-dIAP no2


E-MTAB-2915:esgts control no1

text: public

text: E-MTAB-2915:esgts control no1

text: ArrayExpress

text: fruit fly

text: esgts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgts control no1


E-MTAB-2915:UAS-esg no2

text: public

text: E-MTAB-2915:UAS-esg no2

text: ArrayExpress

text: fruit fly

text: UAS-esg overexpression

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: UAS-esg no2


E-MTAB-2915:esgts control no5

text: public

text: E-MTAB-2915:esgts control no5

text: ArrayExpress

text: fruit fly

text: esgts control

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: esgts control no5


text: University of Zurich

text: public

tag: Namespace:University of Zurich

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: The DLBCL cell lines used were SU-DHL4, SU-DHL6, SU-DHL10, SU-DHL16 and RC-K8 of GC DLBCL subtype and U-2932, Oci-Ly3, Oci-Ly10, SU-DHL2, SU-DHL5 and RIVA of ABC DLBCL as well as SU-DHL7 (unclassified). Cell lines were maintained at 37 degrees C, 5%CO2 in a humidified atmosphere in RPMI or IMDM (RIVA, Oci-Ly10) supplemented with 10% (Oci-Ly10, RIVA, SU-DHL2 and SU-DHL5) or 20% heat-inactivated FBS and antibiotics. CD19 positive B cells were isolated from buffy coats of healthy volunteer blood donors obtained from the blood donation centre Zurich (ZHBSD). The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8-2.1 and a 28S/18S ratio within 1.5-2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


E-MTAB-2925:B cell 57

text: University of Zurich

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2925:B cell 57

text: ArrayExpress

text: CD19-positive B cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: B cell 57


E-MTAB-2925:U2932 AzaPBA

text: University of Zurich

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2925:U2932 AzaPBA

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: U2932 AzaPBA


E-MTAB-2925:B cell 08

text: University of Zurich

text: public

text: E-MTAB-2925:B cell 08

text: ArrayExpress

characteristic: broker name

text: CD19-positive B cell

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: B cell 08


E-MTAB-2925:Oci-ly10 AzaPBA

text: University of Zurich

text: public

text: E-MTAB-2925:Oci-ly10 AzaPBA

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: Oci-ly10 AzaPBA


text: Stowers Institute for Medical Research

text: public

tag: Namespace:Stowers Institute for Medical Research

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: reticulocyte

characteristic: cell type

text: house mouse

text: Protocols: All the mice in this study were kept in C57BL/6J background. All mice used in this study were between 4-6 weeks of age and were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institute of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. RNA was extracted by convention using chloroform- isopropanol trizol method. The RNA-sequencing library was prepared from approximately 200 ng of total RNA for each sample using illumina TruSeq RNA Sample Prep Kit [catalog number: FC-122-1001]). The fragment size in the generated library ranged from 220 to 500 bps with a peak at 280 bps.

text: RFP+ CD45- CD31-Ter119-7AAD-

characteristic: gating

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

text: SDF-RFP


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

text: osteoblast

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 4 to 6 week

text: ArrayExpress

text: mesenchymal cell

text: house mouse

text: YFP+ CD45- CD31-Ter119-7AAD-

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Stowers Institute for Medical Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 4 to 6 week

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

text: Lin-Sca-1+cKit+CD34-Flk2- CD49lo

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: LT-HSC


text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: endothelial cell

text: house mouse

characteristic: common name

characteristic: description

text: GFP+ CD31+ VE-Cadherin+ CD45-Ter119-7AAD-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Pecam-GFP


text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: macrophage

characteristic: cell type

text: house mouse

text: CD45+ F4/80+CD31- Ter119-7AAD-

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Macrophage


characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

text: hematopoietic multipotent progenitor cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

text: MPP


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

text: megakaryocyte

text: house mouse

text: Fschi CD45+ CD41+CD31-Ter119-7AAD-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Megakaryocyte


characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

text: public

text: 4 to 6 week

text: ArrayExpress

text: mesenchymal stem cell

text: house mouse

text: GFP+ CD45- CD31-Ter119-7AAD-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nestin-GFP

characteristic: title


text: Stowers Institute for Medical Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 4 to 6 week

text: ArrayExpress

text: intermediate term hematopoietic stem cell

text: house mouse

text: Lin-Sca-1+cKit+CD34-Flk2- CD49hi

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: IT-HSC


text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: short term hematopoietic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: ST-HSC


text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: immature osteoblast

characteristic: cell type

text: house mouse

characteristic: description

text: RFP+ CD45- CD31-Ter119-7AAD-

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

text: osteoprogenitor

text: house mouse

characteristic: gating

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: N-Cadherin


Paired End BACs barley

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IPK-Gatersleben

text: public

text: Paired End BACs barley

text: domesticated barley

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Paired End BACs barley


BAC lib MP87 HiSeq

characteristic: External Id

text: IPK-Gatersleben

text: public

text: BAC lib MP87 HiSeq

characteristic: Submitter Id

text: domesticated barley

text: library of pooled DNA from barley BACs containing a dilution series of two human BACs (AF252830, AF285443) for test reasons

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: BAC Bank MP87 HiSeq


BAC lib MP87 MiSeq

text: IPK-Gatersleben

characteristic: INSDC center name

text: public

text: BAC lib MP87 MiSeq

text: domesticated barley

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: BAC Bank MP87 MiSeq

characteristic: title


BAC lib MP88 HiSeq

text: IPK-Gatersleben

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: BAC lib MP88 HiSeq

text: domesticated barley

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: BAC Bank MP88 HiSeq


BAC lib MP88 MiSeq

text: IPK-Gatersleben

text: public

characteristic: INSDC status

characteristic: SRA accession

text: BAC lib MP88 MiSeq

text: domesticated barley

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: BAC Bank MP88 MiSeq


text: public

tag: Namespace:Department of Plant Sciences University of Cambridge

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Murine 17 clone 1 cells were maintained in Dulbeccos modification of Eagles medium supplemented with 10% (vol/vol) fetal calf serum. Cells (107) were plated in a 10 cm dish and upon reaching 100% confluence, cycloheximide (Sigma-Aldrich) was added to 100 ug/ml. After 2 min, cells were rinsed with 5 ml of ice-cold PBS, the dishes submerged in a reservoir of liquid nitrogen for 10 sec, transferred to dry ice and 400 ul of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 ug/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies) dripped on. The cells were scraped extensively to ensure lysis, collected and triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 20 min at 13,000 g at 4 C, the supernatants recovered and stored in liquid nitrogen. For mouse samples, lysates were slowly thawed on ice and 250 ul treated with 7.5 ul RNase 1 followed by incubation for 45 min at room temperature on a rotating wheel. 10 ul of SUPERase-In RNase inhibitor was added, the sample layered onto a 1M sucrose cushion in mammalian polysome buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 ug/ml cycloheximide) and ultracentrifuged at 28,000 rpm (16 hr, 4 C) in a Beckman SW55Ti rotor. Subsequently, all ribosome pellets were resuspended in 200 ul of the corresponding polysome buffer and digested with proteinase K (10 mM Tris-HCl pH 7.5, 10% SDS, 200 ug/ml Proteinase K [New England Biolabs]) for 30 min at 42 C. RPFs were recovered by extracting twice with pre-warmed (65 C) acidic phenol:chloroform (Life Technologies) and once with chloroform (1:1, vol/vol, buffered with 10 mM Tris pH 7.5, 0.1 mM EDTA), followed by ethanol precipitation. RPFs were resuspended in 10 mM Tris-HCl pH 7.5 and quantified by spectrophotometry. 150 ul of each cell lysate was digested with proteinase K and cellular RNA extracted using acidic phenol:chloroform as above. Ribosomal RNA was depleted from 5 ug of total RNA using a Ribo-Zero rRNA removal kit targeting the appropriate species following the manufacturers instructions (Human/Mouse/Rat: Epicentre, cat. no. RZH1046, Plant Seed/root: Epicentre, Cat. No. MRZSR116). Depleted RNA was resuspended in 10 mM Tris-HCl pH 7.5 and quantified by spectrophotometry. 1-2 ug of total RNA in 20 ul was mixed with an equal volume of 2X alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3 and 90 mM NaHCO3) and incubated for 15 min at 95 C. The reaction was diluted by addition of 280 ul stop/precipitation solution (300 mM NaOAc pH 5.5, GlycoBlue Co-precipitant [Ambion, 15 mg/ml]), and fragmented RNA recovered by ethanol precipitation. Fragmented total RNA or RPFs (1-2 ug) were separated on 15% (wt/vol) denaturing polyacrylamide gels and RNA species migrating between 28 and 34 nt harvested. RNA was eluted from the gel slices on a rotator overnight at 4 C, in 600 ul RNA gel extraction buffer (300 mM NaOAc pH 5.5, 1 mM EDTA and 0.25% SDS). Eluted RNA was ethanol precipitated. The RNA samples from above were heated at 80 C for 2 min, cooled and the 3' phosphate group removed using T4 polynucleotide kinase (T4 PNK, New England Biolabs) at 37 C for 2 hrs in a 20 ul reaction lacking ATP. The RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl pH 7.5 and ligated in a 20 ul reaction overnight at 14 C to a preadenylated 3'-adaptor (5' rATGGAATTCTCGGGTGCCAAGG 3') using T4 RNA Ligase 2 truncated K227Q (New England Biolabs). This 3' adaptor was adenylated using a 5' DNA adenylation kit (New England Biolabs) following the manufacturers instructions. RNA was precipitated, loaded into a 15% (wt/vol) denaturing polyacrylamide gel and ligated RNA fragments migrating between 49 nt and 53 nt excised. The RNA was eluted, precipitated, resuspended as above and 5' phosphorylated using T4 PNK in the presence of 1mM ATP for 2 hrs at 37 C. RNA was concentrated by ethanol precipitation, resuspended in 10mM Tris-HCl pH 7.5 and ligated to a 5' RNA adaptor (5' rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC 3') in a 20 ul reaction overnight at 14 C using T4 RNA Ligase (Promega). The fully adapted RNAs were recovered by ethanol precipitation, dissolved in 6 ul 10mM Tris-HCl pH 7.5 and 3 ul of this ligated product annealed to an RT primer (5' GCCTTGGCACCCGAGAATTCCA, 50 pmol) at 65 C for 5 min. The RNA was subsequently reverse transcribed at 55 C for 50 min in a 20 ul reaction following addition of first strand buffer (Invitrogen, to 1X), 2.5 mM MgCl2, 10 mM DTT, 0.5 ul SUPERase-In and 1 ul SuperScript III (Invitrogen), followed by heat inactivation at 85C for 5 min. For PCR and ribosomal depletion steps, see referenced manuscript.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MusMus-RNASeq


text: Department of Plant Sciences University of Cambridge

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MusMus-RiboSeq


text: public

tag: Namespace:Department of Molecular Neuroscience, UCL Institute of Neurology

text: ArrayExpress

characteristic: cell type

text: human

text: Protocols: Cells were not treated with siRNA (untreated), treated with anti-STAU1 siRNA (knockdown), or treated with anti-STAU1 siRNA and the STAU1 level was rescued by the expression of siRNA-resistant STAU1 (rescue). Cells were subjected to Cycloheximide treatment before collection. Ribosome profiling protocol was followed to isolate protected RNA from the Cycloheximide teated cells and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction as described in the manuscript. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina paired-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Department of Molecular Neuroscience, UCL Institute of Neurology

text: public

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: A FlpIn293 cell line expressing 3xFLAG-STAU1 was subjected to UV-C irradiation before collection. hiCLIP or iCLIP protocol was followed to isolate RNA bound to 3XFLAG-STAU1 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction, and are specified in the manuscript. Random barcodes were also incorporated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina paired-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium

text: ArrayExpress

text: thale cress

text: Protocols: The rtel1 knockout (rtel1-1) and the Col-0 seeds were germinated on control 1/2MS medium on a nylon mesh. Root tips (less than 2 to 3 mm) were collected and frozen in liquid nitrogen. RNA was extracted from root tissue with the RNeasy plant kit (Qiagen). Illumina True-Seq libraries were generated from cDNA according to the manufacturers protocol and sequenced on a HiSeq2000.

text: germline genotype

characteristic: genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: root tip

characteristic: organism part

text: Arabidopsis thaliana

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium

text: public

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: germline genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: root tip

text: Arabidopsis thaliana


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: thale cress

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: root tip

text: Arabidopsis thaliana

characteristic: title


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Cells were not treated with siRNA (untreated), treated with anti-STAU1 siRNA (knockdown), or treated with anti-STAU1 siRNA and the STAU1 level was rescued by the rescue expression of siRNA-resistant STAU1 (rescue). Cells were subjected to Cycloheximide treatment before collection. RNA-Seq was performed in parallel with ribosome profiling. The protocol was followed to isolate RNA from the Cycloheximide teated cells and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction as described in the manuscript. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina paired-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MTAB-2939:CPSF160_GFP repl2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2939:CPSF160_GFP repl2

tag: Namespace:MRC Laboratory of Molecular Biology, Cambridge

text: ArrayExpress

text: HeLa

characteristic: cell line

text: human

text: Replicate 2 Protocols: iCLIP protocol was followed to isolate RNA bound to CPSF-160 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction and are specified below for each sequencing run. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina pair-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: CPSF160_GFP repl2


E-MTAB-2939:CPSF160_GFP repl1

text: MRC Laboratory of Molecular Biology, Cambridge

text: public

text: E-MTAB-2939:CPSF160_GFP repl1

text: ArrayExpress

text: HeLa

text: human

text: Replicate 1 Protocols: iCLIP protocol was followed to isolate RNA bound to CPSF-160 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction and are specified below for each sequencing run. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina pair-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: CPSF160_GFP repl1


E-MTAB-2939:CPSF160_GFP repl3

text: public

text: E-MTAB-2939:CPSF160_GFP repl3

text: ArrayExpress

text: HeLa

text: human

text: Replicate 3 Protocols: iCLIP protocol was followed to isolate RNA bound to CPSF-160 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction and are specified below for each sequencing run. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina pair-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: CPSF160_GFP repl3


text: public

text: ArrayExpress

text: HeLa

text: human

text: Control Protocols: iCLIP protocol was followed to isolate RNA bound to CPSF-160 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction and are specified below for each sequencing run. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina pair-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Human herpesvirus 4

characteristic: ArrayExpress-Species

text: SC

text: public

text: Epstein-Barr virus

text: Human herpesvirus 4

text: MS patient blood sample

characteristic: sample description

text: Human herpesvirus 4


text: Human herpesvirus 4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Epstein-Barr virus

text: Human herpesvirus 4

text: EBV from cell line

text: Human herpesvirus 4


text: Homo sapiens

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: Wildtype

characteristic: ArrayExpress-Genotype

text: Spleen

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: DNA from cells

text: Mus musculus


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~1 Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Barcoding of nucleosome fractions was performed using 50 ??g of starting material as measured by absorbance at 260nm with Nanodrop. Chromatin fragments were end-repaired with 2 ??L of NEBNext End repair Enzyme Mix (New England BioLabs), dA-tailed with 2 mM dATP and 20U Klenow Fragment (Thermo Scientific) and ligated for 4 hrs at 16??C to paired-end adapters containing a 6-mer multiplex barcode with 1600U T4-DNA Ligase (New England BioLabs). Enzymes were heat-inactivated at 65??C-70??C between each step. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

text: WT

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: gene knock out

characteristic: genetic modification

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~1 Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

text: WT

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me2_1

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me2_2

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~0.5. alpha-factor was added to reach a final concentration of 50ng/mL. Cells were then grown for two generations before harvest. Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

text: gene knock out

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me3_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: title


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_WCE_1

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: gene knock out

characteristic: genetic modification

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K14ac_3

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me3_1

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K14ac_1

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: gene knock out

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me3_3

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: strain


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me3_1

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me2_1

text: ArrayExpress

text: baker's yeast

text: gene knock out

characteristic: genetic modification

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K14ac_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me2_3

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: E-MTAB-2945:sc_htchip_set2_confirm_WCE_3

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: gene knock out

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: WT

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me2_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: title