Series Summary for DCD000407SR

Ntl, Tbx16 and Mixl1 ChIP-seq data : Genome-wide profiling of Ta, Tbx16 and Mixl1 binding in early zebrafish embryos

Survey

10.1016/j.celrep.2017.06.011

GSE84612

Identification of Ta and Tbx16 binding sites during gastrulation, and Mixl1 binding sites during endoderm specification Overall design: Replicate ChIP samples for Ta, Tbx16 and Mixl1 with matched input samples - 6x ChIP samples (2 per factor); 3x input samples

True

aevans

May 21, 2018, 7:17 a.m.

Nov. 7, 2018, 6:37 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007144BS DCD000407SR whole organism Wardle Lab, King's College London AB 30%-epiboly 5
Applied Assay ID Biosample Replicate Assay
DCD002370AA DCD013873BR ChIP-seq_Wardle_Lab_Mixl1_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002743SQ DCD002770TR Wardle Lab, King's College London Illumina HiSeq 1000 unstranded 63 01/01/2012
DCD008300DT: FASTQ
DCD016834DT: BED GRCz10/danRer10
DCD016835DT: BAM GRCz10/danRer10
DCD016836DT: BIGNARROWPEAK GRCz10/danRer10
DCD016837DT: BIGNARROWPEAK GRCz10/danRer10
DCD017277DT: BAM GRCz10/danRer10
DCD017278DT: BIGNARROWPEAK GRCz10/danRer10
DCD017279DT: BED GRCz10/danRer10
DCD017280DT: BIGNARROWPEAK GRCz10/danRer10
DCD017281DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002371AA DCD013873BR ChIP-seq_Wardle_Lab_Mixl1_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002744SQ DCD002769TR Wardle Lab, King's College London Illumina HiSeq 1000 unstranded 63 01/01/2012
DCD008299DT: FASTQ
DCD016830DT: BED GRCz10/danRer10
DCD016831DT: BAM GRCz10/danRer10
DCD016832DT: BIGNARROWPEAK GRCz10/danRer10
DCD016833DT: BIGNARROWPEAK GRCz10/danRer10
DCD017271DT: BIGNARROWPEAK GRCz10/danRer10
DCD017272DT: BED GRCz10/danRer10
DCD017274DT: BAM GRCz10/danRer10
DCD017275DT: BIGNARROWPEAK GRCz10/danRer10
DCD017276DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002368AA DCD013874BR ChIP-seq_Wardle_Lab_input_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002748SQ DCD002772TR Wardle Lab, King's College London Illumina HiSeq 1000 unstranded 63 01/01/2012
DCD008298DT: FASTQ
DCD016972DT: BAM GRCz10/danRer10
DCD017035DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002749SQ DCD002772TR Wardle Lab, King's College London Illumina HiSeq 1000 unstranded 63 01/01/2012
DCD008297DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD007145BS DCD000407SR whole organism Wardle Lab, King's College London AB 75%-epiboly — — 8 —
Applied Assay ID Biosample Replicate Assay
DCD002364AA DCD013875BR ChIP-seq_Wardle_Lab_Tbx16_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002747SQ DCD002771TR Wardle Lab, King's College London Illumina GAIIx unstranded 38 01/01/2010
DCD008293DT: FASTQ
DCD016937DT: BED GRCz10/danRer10
DCD016938DT: BAM GRCz10/danRer10
DCD017404DT: BED GRCz10/danRer10
DCD017405DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002367AA DCD013875BR ChIP-seq_Wardle_Lab_Tbx16_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002745SQ DCD002773TR Wardle Lab, King's College London Illumina GAIIx unstranded 38 01/01/2010
DCD008294DT: FASTQ
DCD016939DT: BAM GRCz10/danRer10
DCD016940DT: BED GRCz10/danRer10
DCD017406DT: BAM GRCz10/danRer10
DCD017407DT: BED GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002366AA DCD013876BR ChIP-seq_Wardle_Lab_Ta_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002746SQ DCD002766TR Wardle Lab, King's College London Illumina GAIIx unstranded 38 01/01/2010
DCD008295DT: FASTQ
DCD016646DT: BED GRCz11/danRer11
DCD016647DT: BAM GRCz11/danRer11
DCD016746DT: BED GRCz10/danRer10
DCD016749DT: BAM GRCz10/danRer10
DCD017160DT: BED GRCz10/danRer10
DCD017163DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002369AA DCD013876BR ChIP-seq_Wardle_Lab_Ta_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002740SQ DCD002774TR Wardle Lab, King's College London Illumina GAIIx unstranded 38 01/01/2010
DCD008296DT: FASTQ
DCD016643DT: BED GRCz11/danRer11
DCD016644DT: BAM GRCz11/danRer11
DCD016747DT: BED GRCz10/danRer10
DCD016748DT: BAM GRCz10/danRer10
DCD017161DT: BAM GRCz10/danRer10
DCD017164DT: BED GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002365AA DCD013877BR ChIP-seq_Wardle_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Paired End Strand Maximum Read Length Sequencing Date
DCD002741SQ DCD002767TR Wardle Lab, King's College London Illumina GAIIx ✘ unstranded 38 01/01/2010
DCD008292DT: FASTQ
DCD016969DT: BAM GRCz10/danRer10
DCD017024DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay Controlled By
DCD002372AA DCD013878BR ChIP-seq_Wardle_Lab_input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002742SQ DCD002768TR Wardle Lab, King's College London Illumina GAIIx — ✔ unstranded 38 01/01/2010
DCD008301DT: FASTQ
DCD016975DT: BAM GRCz10/danRer10
DCD017011DT: BAM GRCz11/danRer11