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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (GTGTCCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


status: PUBLIC

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

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from an embryo heterozygous for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. 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/sanger/Zebrafish_Zmpsearch/zmp_ph150.

characteristic: sample description

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for sox10, allele t3 and heterozygous for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCGTTAGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCCTCAAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TAGTCTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TAACGCTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TACTTCGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTACTCGC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo heterozygous for sox10, allele t3 and wild type for sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTGCGTAC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TACAGGAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTCCATTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTGGTATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


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

text: Whole embryo

text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from an embryo wild type for both sox10, allele t3 and sox10, allele baz1 plus ERCC spike mix 1 (Ambion). The embryos are from clutch 1. A 8 base indexing sequence (TTCAGCTC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph150.

text: Danio rerio


text: Mouse epiblast stem cell

characteristic: ArrayExpress-CellType

text: blastocyst

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

text: blastocyst

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mouse epiblast stem cell

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GIS

text: public

text: ArrayExpress

characteristic: broker name

text: ES-E14 cell

characteristic: cell line

text: house mouse

text: Protocols: Mouse E14 and Oct4-Gip ESCs were plated on 0,1% gelatin coated plates (Sigma G1393) and maintained in DMEM (Invitrogen 11960-044) supplemented with either 15% KSR (Invitrogen 10828-028) or 15% FBS (Hyclone), 1mM L-glutamine (Invitrogen 25030/081), 0,1 mM of non-essential aminoacids (Invitrogen 11140-050), 100 ug/ml penicillin/streptomycin (Invitrogen 15140-122), 1 mM sodium pyruvate (Invitrogen 11360-070), 0,1 mM mercaptoethanol (Sigma M7522), and Esgro 103U/ml (Chemicon ESG1106). Cells were passaged upon reaching 80% confluence. Growth media was aspirated and cells were washed using warm PBS. Cells were dissociated by incubating them with trypsin/EDTA (Invitrogen 15090-046) for 3 to 5 minutes. Once most of the cells are observed to be at a single cell dissociation state, they were collected and spun down for 5 minutes at 1200 rpms. After pellet ressuspention cells were plated in a gelatin coated plated at an average density of 21000 cells per cm2 . Embryoid bodies were formed by plating ES cells in non-attachment conditions (suspension culture) with ES cell medium with fetal bovine serum and in the absence of Esgro, for 21 days. ChIP-qPCR was performed as described by Upstate Biotechnology with minor adaptations: cells were first crosslinked with 1.5mM EGS (proteochem-c1130-100mg) per 10 ml of iced PBS, cells were incubated on a nutator for 45 minutes. After 3 PBS washes cells are crosslinked with 1% formaldehyde for 10 mins with soft orbital agitation. Formaldehyde is quenched with 250 mM of glycine for 5 minutes and triple washed with PBS. Cells were sonicated post lysis in a bioruptor for 40 min total (7 sec on/15 sec off on high). Immunoprecipitation was achieved using an anti-NRF1 antibody (ab34682) and with an IgG control (ab46540). DNA was extracted using qiagen PCR purification kit.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title

type: has member


text: GIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: ES-E14 cell

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Control


text: GIS

text: public

text: ArrayExpress

text: ES-E14 cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PolII


text: UPPSALA UNIVERSITET

text: public

tag: Namespace:UPPSALA UNIVERSITET

text: American crow

text: Corvus brachyrhynchos

text: Corvus brachyrhynchos


text: UPPSALA UNIVERSITET

text: public

text: hooded crow

text: Corvus cornix

text: Corvus cornix


text: UPPSALA UNIVERSITET

text: public

text: rook

text: Corvus frugilegus

text: Corvus frugilegus


text: UPPSALA UNIVERSITET

text: public

text: jackdaw

text: Corvus monedula

text: Corvus monedula


text: UPPSALA UNIVERSITET

text: public

text: collared crow

text: Corvus pectoralis

text: Corvus pectoralis


text: UPPSALA UNIVERSITET

text: public

text: Corvus corone orientalis X Corvus cornix

text: Corvus corone orientalis

text: Corvus corone orientalis


characteristic: ArrayExpress-CellType

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: SMARTSeq2 amplified cDNA

characteristic: sample description

text: Mus musculus


text: male

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: SMARTSeq2 amplified cDNA

text: Mus musculus


text: female

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Picoplex amplified gDNA

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Picoplex amplified gDNA

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: PBAT libraries of mouse ESCs E14 G7

text: Mus musculus

characteristic: strain


text: female

text: Homo Sapien

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: PBAT libraries of human ESCs H9

text: Homo sapiens


characteristic: ArrayExpress-Compound

text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

characteristic: ArrayExpress-DevelopmentalStage

text: 0.5 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 0_5BRAF_0_1DMSO_28hpf_treated_1-sc-2268051

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 0_5BRAF_0_1DMSO_28hpf_treated_3-sc-2268052

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_4-sc-2268053

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_5-sc-2268054

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_6-sc-2268055

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 0_5BRAF_0_1DMSO_28hpf_treated_7-sc-2268056

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 0_5BRAF_0_1DMSO_28hpf_treated_8-sc-2268057

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_9-sc-2268058

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_10-sc-2268059

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 0.5 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 0_5BRAF_0_1DMSO_28hpf_treated_11-sc-2268060

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 0.5 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 0_5BRAF_0_1DMSO_28hpf_treated_12-sc-2268061

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.5 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 1BRAF_0_1DMSO_28hpf_treated_1-sc-2268062

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGGTTGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_2-sc-2268063

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_3-sc-2268064

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_4-sc-2268065

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 1BRAF_0_1DMSO_28hpf_treated_5-sc-2268066

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 1BRAF_0_1DMSO_28hpf_treated_6-sc-2268067

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_7-sc-2268068

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_8-sc-2268069

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_9-sc-2268070

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 1BRAF_0_1DMSO_28hpf_treated_10-sc-2268071

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 1BRAF_0_1DMSO_28hpf_treated_11-sc-2268072

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 1 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 1BRAF_0_1DMSO_28hpf_treated_12-sc-2268073

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 1 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTGACTCT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_1-sc-2268074

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

characteristic: ArrayExpress-DevelopmentalStage

text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_2-sc-2268075

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTCCTGCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 2BRAF_0_1DMSO_28hpf_treated_3-sc-2268076

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TAGTGACT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 2BRAF_0_1DMSO_28hpf_treated_4-sc-2268077

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TACAGGAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_5-sc-2268078

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCCTCAAT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_6-sc-2268079

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_7-sc-2268080

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TAGTCTTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

characteristic: ArrayExpress-Dose

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 2BRAF_0_1DMSO_28hpf_treated_8-sc-2268081

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTCCATTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: 2BRAF_0_1DMSO_28hpf_treated_9-sc-2268082

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_10-sc-2268083

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TAACGCTG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_11-sc-2268084

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TTGGTATG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: 2 uM in 0.1% v/v DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2BRAF_0_1DMSO_28hpf_treated_12-sc-2268085

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 2 micromolar CHEMBL2105729 in 0.1% v/v DMSO. A 8 base indexing sequence (TGAACTGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TACTTCGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TCCAGTCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: DMSO

characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

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 single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TCATTGAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TGGCTCAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_control_10-sc-2268095

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TCAGATTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: DMSO

text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_control_11-sc-2268096

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TACTAGTC) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: DMSO

characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_control_12-sc-2268097

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo treated with 0.1% v/v DMSO.A 8 base indexing sequence (TTCAGCTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: BRAF_0_1DMSO_28hpf_untreated_1-sc-2268098

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: BRAF_0_1DMSO_28hpf_untreated_2-sc-2268099

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_3-sc-2268100

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_4-sc-2268101

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_6-sc-2268102

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single wild type 28hpf embryo. A 8 base indexing sequence (TGTTCTCC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_7-sc-2268103

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. A 8 base indexing sequence (TTCGCACC) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Pharyngula : Prim 5-Prim 15 - ZFS:0000029 - ZFS:0000030

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_8-sc-2268104

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. A 8 base indexing sequence (TTGCGTAC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: BRAF_0_1DMSO_28hpf_untreated_9-sc-2268105

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: BRAF_0_1DMSO_28hpf_untreated_10-sc-2268106

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

characteristic: SRA accession

text: BRAF_0_1DMSO_28hpf_untreated_11-sc-2268107

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: BRAF_0_1DMSO_28hpf_untreated_12-sc-2268108

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single wild type 28hpf embryo. 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: Tasmanian Devil

characteristic: ArrayExpress-Phenotype

text: Sarcophilus harrisii

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Tasmanian devil

text: Sarcophilus harrisii

text: Sarcophilus harrisii


E-MTAB-3465:mES Biological replicate 2

characteristic: ENA-LAST-UPDATE

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES Biological replicate 2

tag: Namespace:Massachusetts Institute of Technology

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

characteristic: common name

text: Protocols: Mouse embryonic stem cell culture and endoderm differentiation was modified slightly from previously published protocols (PMID: 15020474). Undifferentiated 129P2/OlaHsd mouse ES cells were maintained on gelatin-coated plates with mouse embryonic fibroblast (MEF) feeders in mES media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (Life Technologies), Glutamax (Life Technologies), 0.55mM 2-mercaptoethanol (Sigma), and 1X ESGRO LIF (Millipore). Cells were regularly tested for mycoplasma and normal karyotype. Prior to differentiation, ES cells were passaged onto gelatin-coated plates for 25 minutes to deplete MEFs. MEF-depleted ES cells were then seeded at 1X10e4 cells/cm2 onto gelatin- coated dishes in mES media. After 12-24 hours, media was changed to Advanced DMEM (Life Technologies) supplemented with N-2 (Life Technologies), B27 Supplement without vitamin A (Life Technologies), and Glutamax. After 44-48 hours, media was changed to Advanced DMEM with 2% FBS, Glutamax, 5 nM GSK-3 inhibitor XV and 50 ng/mL E. coli-derived Activin A (Peprotech) for 24 hours to produce mesendoderm. For endoderm differentiation, cells were then fed with Advanced DMEM with 2% FBS, Glutamax, 50 ng/mL Activin A and 1 uM Dorsomorphin (Sigma) for 48 hours. For intestinal endoderm differentiation, cells at the endoderm stage were fed for 24 hours with Advanced DMEM with B-27 supplement without vitamin A, Glutamax, and 100 nM GSK-3 inhibitor XV. For pre-pancreatic endoderm differentiation, cells at the endoderm stage were fed for 24 hours with Advanced DMEM with B- 27 supplement without vitamin A, Glutamax, 500 nM retinoic acid (Calbiochem), 50 nM A-83-01 (Calbiochem), and 8 ng/mL Bmp4 (Stemgent). For mesodermal differentiation, cells at the mesendoderm stage were treated for 48 hours with 10 ng/mL Bmp4. ES cells with doxycycline-inducible alleles for Sox2, Foxa1, Hnf1beta, Cdx2, Gata6, Zfp161, and Klf7 in the HPRT locus were created as described (PMID: 22955985) and maintained and differentiated as above. For dominant negative lines, DNA-binding domains of NFYA and Nrf1 were used to create doxycycline-inducible HPRT lines as above. Dominant negative lines were grown for >7 days in mES media supplemented with 5 nM GSK-3 inhibitor XV and 500 nM UO126 to enhance pluripotency37 and 2 ug/mL Doxycycline. Cells were harvested at this stage for DNase-qPCR. For ChIP-qPCR, cells were treated for 6 hours with mES media with 1 uM retinoic acid. Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80C for a later digestion. If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 10e7 nuclei. Volumes should be scaled as per cell number. Digestion buffer (850 ul per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 ul per 10e7 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 ug/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37C. DNaseI enzyme was combined with warmed digestion buffer for a final volume of 100 ul per 107 nuclei. If multiple concentrations of DNaseI were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37C. Pre- warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2ug/mL and samples were incubated overnight at 55C. DNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20C for 5-6 hours or at -80C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer. To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the 150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control). DNA samples are confirmed using the Advanced Analytical Fragment Analyzer (FA) and prepared for sequencing using standard Illumina ligation based library construction on a SPRIworks system (Beckman Coulter Genomics). Ligated fragments are amplified for 8-16 cycles of PCR using standard Illumina primers containing molecular indexes. Final libraries are quantified on the FA and by qPCR before pooling and sequencing.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES Biological replicate 2

characteristic: title


name: E-MTAB-3465:mES for 'Day6' differentiated cells (beta cell protocol)

characteristic: External Id

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


E-MTAB-3465:mES Biological replicate 1

text: Massachusetts Institute of Technology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3465:mES Biological replicate 1

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES Biological replicate 1


name: E-MTAB-3465:mES for 'Day2' differentiated cells (beta cell protocol)

text: Massachusetts Institute of Technology

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3465:mES for 'Day3' differentiated cells (beta cell protocol)

text: Massachusetts Institute of Technology

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3465:mES for 'Day7' differentiated cells (anterior endoderm lineage)

characteristic: ENA-CHECKLIST

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3465:mES for 'Day5' differentiated cells (variant protocol)

text: Massachusetts Institute of Technology

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3465:mES for Ph3s10/PFA+

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES for Ph3s10/PFA+

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES for Ph3s10/PFA+


name: E-MTAB-3465:mES for 'Day5' differentiated cells (beta cell protocol)

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3465:mES 'Day6' differentiated cells (intestinal lineage)

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3465:mES for Ph3s10/PFA+/Noco+

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES for Ph3s10/PFA+/Noco+

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES for Ph3s10/PFA+/Noco+


name: E-MTAB-3465:mES for 'Day7' differentiated cells (beta cell protocol)

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3465:mES for 'Day6' differentiated cells (intestinal lineage)

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3465:mES for NFYAdn+

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES for NFYAdn+

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES for NFYAdn+


E-MTAB-3465:mES for Ph3s10/PFA-

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES for Ph3s10/PFA-

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES for Ph3s10/PFA-


E-MTAB-3465:mES for 9h Noco

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3465:mES for 9h Noco

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES for 9h Noco


E-MTAB-3468:Whole mouse embryo 2

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3468:Whole mouse embryo 2

characteristic: age

text: ArrayExpress

text: house mouse

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

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain or line

text: Whole mouse embryo 2


E-MTAB-3468:Whole mouse embryo

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3468:Whole mouse embryo

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Whole mouse embryo


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 pancreas

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Small RNA's were size fractionated from total RNA based on charge. Capped transcripts were enriched by immunoprecipitation and poly-A selected with Oligo dT. An enzymatic cocktail was applied to modify the RNA's for use with the NEBNext Kit. Please contact the investigators for further information. NA

text: Mus musculus

text: Mus musculus

text: pancreas

characteristic: organism part

text: Mus musculus

text: SW outbred F

text: Mouse (SW outbred F) E14.5 pancreas


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 liver

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: SW outbred F

text: Mouse (SW outbred F) E14.5 liver


E-MTAB-3489:Hues8 S1

characteristic: External Id

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3489:Hues8 S1

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: See Hrvatin et al. 10.1073/pnas.1400709111 SI Experimental Procedures. Small RNA's were size fractionated from total RNA based on charge. Capped transcripts were enriched by immunoprecipitation and poly-A selected with Oligo dT. An enzymatic cocktail was applied to modify the RNA's for use with the NEBNext Kit. Please contact the investigators for further information. NA

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Hues8 S1

characteristic: title


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 brain pool

text: Massachusetts Institute of Technology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: Mus musculus

text: SW outbred F

text: Mouse (SW outbred F) E14.5 brain pool


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 liver pool

text: Massachusetts Institute of Technology

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: SW outbred F

text: Mouse (SW outbred F) E14.5 liver pool


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 pancreas pool

characteristic: ENA-CHECKLIST

text: Massachusetts Institute of Technology

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: pancreas

text: Mus musculus

text: SW outbred F


name: E-MTAB-3489:Mouse (SW outbred F) E14.5 brain

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Massachusetts Institute of Technology

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: SW outbred F

characteristic: strain or line

text: Mouse (SW outbred F) E14.5 brain


E-MTAB-3489:Hues8 S3

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3489:Hues8 S3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Hues8 S3


E-MTAB-3489:Hues8 S2

characteristic: External Id

text: Massachusetts Institute of Technology

text: public

text: E-MTAB-3489:Hues8 S2

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Hues8 S2


characteristic: ArrayExpress-DevelopmentalStage

text: WT

characteristic: ArrayExpress-Genotype

text: MUS MUSCULUS

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: strain


E-MTAB-3452:Sample 11

text: Centre for Human Genetics KU Leuven

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3452:Sample 11

tag: Namespace:Centre for Human Genetics KU Leuven

text: ArrayExpress

text: rabbit

text: Protocols: total 8 does were weighed and premedicated with ketamine 50 mg/kg kg (Ketamine 1000 CEVA; CEVA Sante Animale, Brussels, Belgium), xylazine 6 mg/kg (Vexylan; CEVA Sante Animale), and Buprenorphine 0.03 mg/kg (Vetergesic; Reckitt Benckiser Healthcare, Brussels, Belgium), all injected intramuscularly. General anesthesia was maintained using a face mask with isoflurane 1.5% (Isoba Vet; Abbott Laboratories Ltd., Queenborough, Kent, UK) in oxygen at 1 L/min. Maternal heart rate and oxygen saturation were monitored with a pulse oxymeter (Nellcor N-20P; Nellcor Inc., Haasrode, Belgium). Body temperature was maintained by a heating pad. The doe was placed in the supine position, the abdominal wall was shaved and disinfected with povidone iodine (Isobetadine; Asta Medica, Brussels, Belgium) and draped in a sterile fashion. Throughout all surgical procedures aseptic conditions were maintained. In every doe we operated on two fetuses each in the middle of the left or right uterine horn. First diaphragmatic hernia (DH) was created at 23 days' GA. A second operation was performed on these DH fetuses at 28 days' GA. At that time, one fetus underwent tracheal occlusion (TO group), whereas another underwent a sham operation (DH group), i.e. hysterotomy, fetal neck exposure, tracheal dissection without ligation, and skin closure. The latter is performed to exclude the effects of a fetal surgical procedure per se. At 30 days' GA, the does were euthanized and all operated fetuses and 1 control nonoperated littermate (WT) were harvested by cesarean section to obtain nonventilated lungs. total 8 does were weighed and premedicated with ketamine 50 mg/kg kg (Ketamine 1000 CEVA; CEVA Sante Animale, Brussels, Belgium), xylazine 6 mg/kg (Vexylan; CEVA Sante Animale), and Buprenorphine 0.03 mg/kg (Vetergesic; Reckitt Benckiser Healthcare, Brussels, Belgium), all injected intramuscularly. General anesthesia was maintained using a face mask with isoflurane 1.5% (Isoba Vet; Abbott Laboratories Ltd., Queenborough, Kent, UK) in oxygen at 1 L/min. Maternal heart rate and oxygen saturation were monitored with a pulse oxymeter (Nellcor N-20P; Nellcor Inc., Haasrode, Belgium). Body temperature was maintained by a heating pad. The doe was placed in the supine position, the abdominal wall was shaved and disinfected with povidone iodine (Isobetadine; Asta Medica, Brussels, Belgium) and draped in a sterile fashion. Throughout all surgical procedures aseptic conditions were maintained. In every doe we operated on two fetuses each in the middle of the left or right uterine horn. First diaphragmatic hernia (DH) was created at 23 days' GA. A second operation was performed on these DH fetuses at 28 days' GA. At that time, one fetus underwent tracheal occlusion (TO group), whereas another underwent a sham operation (DH group), i.e. hysterotomy, fetal neck exposure, tracheal dissection without ligation, and skin closure. The latter is performed to exclude the effects of a fetal surgical procedure per se. At 30 days' GA, the does were euthanized and all operated fetuses and 1 control nonoperated littermate (WT) were harvested by cesarean section to obtain nonventilated lungs. RNA isolation was performed on the whole left lung samples within 4hrs of harvesting using the RNeasy mini kit (Qiagen Benelux B.V., Venlo NL ). Tissue lysis and homogenization was performed in 1200ul Buffer RLT using the TissueLyser system (Qiagen Benelux B.V., Venlo NL). One ug of total RNA was used as input material for sequencing library preparation which was performed with the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturers protocol. Fragmentation was performed for 6 mins. 8 PCR cycles were used for PCR enrichment step. Samples were indexed to allow for multiplexing.

text: fetal

characteristic: developmental stage

text: normal

characteristic: disease

text: 30 day

characteristic: gestational age

text: Oryctolagus cuniculus

characteristic: organism

text: Oryctolagus cuniculus

text: left lung

characteristic: organism part

text: Oryctolagus cuniculus

text: Sample 11

characteristic: title


text: Normal

characteristic: ArrayExpress-Phenotype

text: Saccharomyces cerevisiae

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: sample description

text: Saccharomyces cerevisiae


E-MTAB-3497:mES culture

text: Massachusetts Institute of Technology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3497:mES culture

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

text: Protocols: Mouse embryonic stem cell culture and endoderm differentiation was modified slightly from previously published protocols (PMID: 15020474). Undifferentiated 129P2/OlaHsd mouse ES cells were maintained on gelatin-coated plates with mouse embryonic fibroblast (MEF) feeders in mES media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (Life Technologies), Glutamax (Life Technologies), 0.55mM 2-mercaptoethanol (Sigma), and 1X ESGRO LIF (Millipore). Cells were regularly tested for mycoplasma and normal karyotype. Prior to differentiation, ES cells were passaged onto gelatin-coated plates for 25 minutes to deplete MEFs. MEF-depleted ES cells were then seeded at 1X10e4 cells/cm2 onto gelatin- coated dishes in mES media. After 12-24 hours, media was changed to Advanced DMEM (Life Technologies) supplemented with N-2 (Life Technologies), B27 Supplement without vitamin A (Life Technologies), and Glutamax. After 44-48 hours, media was changed to Advanced DMEM with 2% FBS, Glutamax, 5 nM GSK-3 inhibitor XV and 50 ng/mL E. coli-derived Activin A (Peprotech) for 24 hours to produce mesendoderm. For endoderm differentiation, cells were then fed with Advanced DMEM with 2% FBS, Glutamax, 50 ng/mL Activin A and 1 uM Dorsomorphin (Sigma) for 48 hours. For intestinal endoderm differentiation, cells at the endoderm stage were fed for 24 hours with Advanced DMEM with B-27 supplement without vitamin A, Glutamax, and 100 nM GSK-3 inhibitor XV. For pre-pancreatic endoderm differentiation, cells at the endoderm stage were fed for 24 hours with Advanced DMEM with B- 27 supplement without vitamin A, Glutamax, 500 nM retinoic acid (Calbiochem), 50 nM A-83-01 (Calbiochem), and 8 ng/mL Bmp4 (Stemgent). For mesodermal differentiation, cells at the mesendoderm stage were treated for 48 hours with 10 ng/mL Bmp4. ES cells with doxycycline-inducible alleles for Sox2, Foxa1, Hnf1beta, Cdx2, Gata6, Zfp161, and Klf7 in the HPRT locus were created as described (PMID: 22955985) and maintained and differentiated as above. For dominant negative lines, DNA-binding domains of NFYA and Nrf1 were used to create doxycycline-inducible HPRT lines as above. Dominant negative lines were grown for >7 days in mES media supplemented with 5 nM GSK-3 inhibitor XV and 500 nM UO126 to enhance pluripotency37 and 2 ug/mL Doxycycline. Cells were harvested at this stage for DNase-qPCR. For ChIP-qPCR, cells were treated for 6 hours with mES media with 1 uM retinoic acid. Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80C for a later digestion. If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4 degrees C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 10e7 nuclei. Volumes should be scaled as per cell number. Digestion buffer (850 ul per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 ul per 10e7 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 ug/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37C. DNaseI enzyme was combined with warmed digestion buffer for a final volume of 100 ul per 107 nuclei. If multiple concentrations of DNaseI were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37C. Pre- warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2ug/mL and samples were incubated overnight at 55C. CDNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20C for 5-6 hours or at -80C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer. To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the 150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control). For regions of interest within the mouse reference genome, oligonucleotides were synthesized and used as baits. Post-size selection DNA fragments that hybridized were then selected and amplified for downstream sequencing. Please contact the investigators for further information. DNA samples are confirmed using the Advanced Analytical Fragment Analyzer (FA) and prepared for sequencing using standard Illumina ligation based library construction on a SPRIworks system (Beckman Coulter Genomics). Ligated fragments are amplified for 8-16 cycles of PCR using standard Illumina primers containing molecular indexes. Final libraries are quantified on the FA and by qPCR before pooling and sequencing.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: mES culture


text: Epithelial Cell

characteristic: ArrayExpress-CellType

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: FVB/N

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA

text: Mus musculus

text: FVB/N

characteristic: strain


text: Epithelial Cell

text: male

text: Mus musculus

text: FVB/N

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: RNA

text: Mus musculus

text: FVB/N


text: University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:University of Cambridge

characteristic: Submitter Id

text: ArrayExpress

text: fission yeast

characteristic: common name

text: Protocols: 200 ml of cells were grown at 32 degree C to a density of 1E7 cells/ml Cells were fixed by the addition of formaldehyde to a final concentration of 1%, followed by incubation for 30 minutes at 32 degree C. The reaction was stopped with 10 ml of 2.5 M glycine. Cells were washed extensively in phosphate-buffered saline solution (PBS), resuspended in lysis buffer (50 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1% Triton X-100, 1 mM PMSF, and 1× complete protease inhibitor cocktail [Roche]), and lysed with a Fastprep 24 bead-beater (5 cycles of 20 seconds at level 6.5). Chromatin was sheared by sonication with a Bioruptor (Diagenode; 6 cycles of 5 minutes with 30 seconds on / 30 seconds off at high intensity). The lysates were cleared by centrifugation at 20,000 g for 10 minutes, and adjusted to 500 ul at 6 ug/ul total protein, as determined by the BCA assay. 100 ul of magnetic beads (Pan Mouse IgG or protein G, Life Technologies) were blocked with bovine serum albumin (BSA), and coated with 5 ug of mouse monoclonal antibodies against methylated H3K9 (H3K9me2, Abcam ab1120) or with anti-histone H3 rabbit polyclonal antibodies (Abcam ab1791), respectively. The extracts were incubated overnight with the coated beads at 4 degree C with rotation. Next, the beads were washed twice with 0.8 ml of 50 mM HEPES pH 7.6, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate, twice in the same buffer containing 500 mM NaCl, twice in 10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate, and once in Tris-EDTA solution. Elution and crosslinking reversal were performed by incubating the beads in 200 ul of 10 mM Tris-HCl pH 8, 1 mM EDTA, and 1% SDS overnight at 65 degree C. DNA was purified with Qiagen's a MinElute PCR purification kit (Qiagen) following the manufacturer’s protocol, and eluted in 10 ul. Libraries were prepared using the Next ChIP-seq Library Prep Master Mix Set for Illumina (New England Biolabs) according to the manufacturer’s instructions

characteristic: genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

characteristic: title


text: University of Cambridge

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: fission yeast

characteristic: description

text: wild type

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe