Series Summary for DCD000186SR

Pou5f3 and Sox2 ChIP-seq

Survey

10.1126/science.1242527

GSE39780

Zebrafish homologues of the mammalian core pluripotency factors, Pou5f3 and SoxB1 are also crucially involved in Zygotic Genome Activation in zebrafish. To identify the components of Pou5f3 and SoxB1-dependent transcriptional networks, Wolfgang Driever lab determined the genomic binding sites for Pou5f3 at 512 cell stage and 50% epiboly and Sox2 at 50% epiboly stage using ChIP-seq. For Pou5f3 Chip-seq, MZspg mutant embryos, injected with 25 pg/embryo synthetic Flag-Pou5f3 mRNA and anti-Flag antibody were used. For Sox2 ChIp-seq, AB/TL zebrafish embryos and anti-Sox2 antibody were used. 76-basepair single-end reads of 50% epiboly Pou5f3 (twice, to reach the deeper read density) and Sox2 ChIP-seq and input control were sequenced the Genome Analyzer IIx (Illumina), resulting in 4 FASTQ files for ChIP-seq: one for Sox2 and for Input control, and two for Pou5f3. For the pre-MBT Pou5f3 ChIP samples, 51-basepair single-end reads were sequenced by GATC Biotech AG using a HighSeq 2000 (Illumina), resulting in 1 additional FASTQ file for ChIP-seq

True

Onichtchouk

May 30, 2016, 5:20 a.m.

Nov. 7, 2018, 5:15 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Treatment Hours Post Fertilization Mutation Description
DCD006516BS DCD000186SR whole organism Driever Lab, University of Freiburg AB/TL 50%-epiboly 5
Applied Assay ID Biosample Replicate Assay
DCD001185AA DCD012638BR ChIP-seq_Driever_Lab_Sox2_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD000974SQ DCD001185TR Driever Lab, University of Freiburg Illumina GAIIx unstranded 76 05/05/2012
DCD000630DT: FASTQ
DCD008951DT: BIGNARROWPEAK GRCz10/danRer10
DCD009057DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001188AA DCD012642BR ChIP-seq_Driever_Lab_Input control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD000975SQ DCD001184TR Driever Lab, University of Freiburg Illumina GAIIx unstranded 76 05/05/2012
DCD000634DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Treatment Hours Post Fertilization Mutation Description
DCD006517BS DCD000186SR whole organism Driever Lab, University of Freiburg AB/TL 512-cell pou5f3_mRNA 2.75 m793 MZspg
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001186AA DCD012641BR ChIP-seq_Driever_Lab_Pou5f3_0004AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD000971SQ DCD001181TR Driever Lab, University of Freiburg Illumina HiSeq 2000 unstranded 51 04/04/2013
DCD000633DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Anatomical Term Treatment Hours Post Fertilization Mutation Description
DCD006518BS DCD000186SR whole organism Driever Lab, University of Freiburg AB/TL 50%-epiboly pou5f3_mRNA 5 m793 MZspg
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001187AA DCD012640BR ChIP-seq_Driever_Lab_Pou5f3_0004AS DCD001188AA
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD000973SQ DCD001183TR Driever Lab, University of Freiburg Illumina GAIIx unstranded 76 05/05/2012
DCD000631DT: FASTQ
DCD008950DT: BIGNARROWPEAK GRCz10/danRer10
DCD009058DT: BIGWIG GRCz10/danRer10
DCD016200DT: BIGNARROWPEAK GRCz11/danRer11
DCD016201DT: BIGNARROWPEAK GRCz11/danRer11
DCD016203DT: BED GRCz11/danRer11
DCD016204DT: BIGWIG GRCz11/danRer11
DCD016209DT: BAM GRCz11/danRer11
DCD016665DT: BED GRCz10/danRer10
DCD016667DT: BIGNARROWPEAK GRCz10/danRer10
DCD016668DT: BAM GRCz10/danRer10
DCD016669DT: BIGNARROWPEAK GRCz10/danRer10
DCD017061DT: BIGNARROWPEAK GRCz10/danRer10
DCD017062DT: BIGNARROWPEAK GRCz10/danRer10
DCD017063DT: BED GRCz10/danRer10
DCD017065DT: BAM GRCz10/danRer10
DCD017066DT: BIGWIG GRCz10/danRer10
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD000972SQ DCD001182TR Driever Lab, University of Freiburg Illumina GAIIx unstranded 76 05/05/2012
DCD000632DT: FASTQ