Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq of the HOXA9 and MEIS1 transcription factors in SEM cells.

ABSTRACT: SEM cells were established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia (ALL). SEM cells exhibit the t(4;11) chromosomal rearrangement, which leads to production of the MLL-AF4 fusion protein. Hematopoietic transcription factors including HOXA9 and MEIS1 are highly expressed in ALL. ChIP-seq was performed against HoxA9 and MEIS1 in SEM cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Young

PROVIDER: E-GEOD-38339 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:modENCODE_submission_3606 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP57(official name : OP57 genotype : unc-119(ed3); wgIs57(sem-4::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The SEM-4::EGFP fusion protein is expressed in the correct sem-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sem-4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc-119(ed3); wgIs57(sem-4::TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene sem-4; Strain OP57(official name : OP57 genotype : unc-119(ed3); wgIs57(sem-4::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The SEM-4::EGFP fusion protein is expressed in the correct sem-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sem-4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

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ChIP-seq of the HOXA9 and MEIS1 transcription factors in SEM cells.

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