Series Summary for DCD000428SR

Systemic gain and loss of chromatin architecture throughout zebrafish development

Survey

10.1016/j.celrep.2018.06.003

GSE105015

genome-wide HiC for embryos across four developmental stages (2, 4, 8 and 24hpf). 4C-seq for embryos across two developmental stages (4 and 24 hours after fertilization). Overall design: to explore the 3D genome reorganization during development, the authors performed hiC experiments across four stages of development. To confirm observations in HiC data, the authors performed 12 viewpoints 4C-seq experiments at putative enhancers, at TSSs, and close to TAD boundaries in embryos of 4 and 24hpf

True

irene.stevens

July 17, 2018, 2:56 a.m.

Nov. 15, 2018, 7:56 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007247BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL Prim-5 24
Applied Assay ID Biosample Replicate Assay
DCD002656AA DCD014017BR 4C-seq_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003028SQ DCD003067TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/02/2018
DCD010933DT: FASTQ
DCD010934DT: FASTQ
DCD010935DT: FASTQ
DCD010936DT: FASTQ
DCD010937DT: FASTQ
DCD010938DT: FASTQ
DCD010939DT: FASTQ
DCD010940DT: FASTQ
DCD010941DT: FASTQ
DCD010942DT: FASTQ
DCD010943DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007248BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL Prim-5 24
Applied Assay ID Biosample Replicate Assay
DCD002657AA DCD014018BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003006SQ DCD003053TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD010956DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003033SQ DCD003052TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD010957DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002647AA DCD014022BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003014SQ DCD003071TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010968DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003021SQ DCD003062TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010966DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003031SQ DCD003046TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010972DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003003SQ DCD003031TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010970DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002648AA DCD014023BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003025SQ DCD003073TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010964DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003041SQ DCD003072TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010963DT: FASTQ
DCD011092DT: BIGWIG GRCz10/danRer10
DCD011093DT: BIGWIG GRCz10/danRer10
DCD011094DT: BIGWIG GRCz10/danRer10
DCD011095DT: BIGWIG GRCz10/danRer10
DCD011096DT: BIGWIG GRCz10/danRer10
DCD011097DT: BIGWIG GRCz10/danRer10
DCD011103DT: COOL GRCz10/danRer10
DCD017476DT: BIGWIG GRCz11/danRer11
DCD017477DT: BIGWIG GRCz11/danRer11
DCD017478DT: BIGWIG GRCz11/danRer11
DCD017479DT: BIGWIG GRCz11/danRer11
DCD017480DT: BIGWIG GRCz11/danRer11
DCD017481DT: BIGWIG GRCz11/danRer11
DCD017487DT: COOL GRCz11/danRer11
DCD017524DT: BIGWIG GRCz11/danRer11
DCD017525DT: BIGWIG GRCz11/danRer11
DCD017526DT: BIGWIG GRCz11/danRer11
DCD017527DT: BIGWIG GRCz11/danRer11
DCD017528DT: BIGWIG GRCz11/danRer11
DCD017529DT: BIGWIG GRCz11/danRer11
DCD017535DT: BIGWIG GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003036SQ DCD003070TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010960DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003024SQ DCD003066TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010962DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007249BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL Dome 4
Applied Assay ID Biosample Replicate Assay
DCD002658AA DCD014019BR 4C-seq_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003032SQ DCD003045TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/02/2018
DCD010944DT: FASTQ
DCD010945DT: FASTQ
DCD010946DT: FASTQ
DCD010947DT: FASTQ
DCD010948DT: FASTQ
DCD010949DT: FASTQ
DCD010950DT: FASTQ
DCD010951DT: FASTQ
DCD010952DT: FASTQ
DCD010953DT: FASTQ
DCD010955DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007250BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL Dome 4
Applied Assay ID Biosample Replicate Assay
DCD002654AA DCD014015BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003030SQ DCD003047TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011022DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003012SQ DCD003038TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011032DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003015SQ DCD003036TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011027DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003017SQ DCD003035TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011030DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003016SQ DCD003030TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011023DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003027SQ DCD003029TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011025DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002651AA DCD014016BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002999SQ DCD003069TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011019DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003013SQ DCD003068TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011017DT: FASTQ
DCD011098DT: BIGWIG GRCz10/danRer10
DCD011099DT: BIGWIG GRCz10/danRer10
DCD011100DT: BIGWIG GRCz10/danRer10
DCD011101DT: BIGWIG GRCz10/danRer10
DCD011102DT: BIGWIG GRCz10/danRer10
DCD011104DT: BIGWIG GRCz10/danRer10
DCD011109DT: COOL GRCz10/danRer10
DCD017482DT: BIGWIG GRCz11/danRer11
DCD017483DT: BIGWIG GRCz11/danRer11
DCD017484DT: BIGWIG GRCz11/danRer11
DCD017485DT: BIGWIG GRCz11/danRer11
DCD017486DT: BIGWIG GRCz11/danRer11
DCD017488DT: BIGWIG GRCz11/danRer11
DCD017493DT: COOL GRCz11/danRer11
DCD017530DT: BIGWIG GRCz11/danRer11
DCD017531DT: BIGWIG GRCz11/danRer11
DCD017532DT: BIGWIG GRCz11/danRer11
DCD017533DT: BIGWIG GRCz11/danRer11
DCD017534DT: BIGWIG GRCz11/danRer11
DCD017536DT: BIGWIG GRCz11/danRer11
DCD017541DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007251BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL 75%-epiboly 8
Applied Assay ID Biosample Replicate Assay
DCD002650AA DCD014024BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003029SQ DCD003059TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010980DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003034SQ DCD003058TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010989DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003007SQ DCD003057TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010987DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003001SQ DCD003056TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010986DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003002SQ DCD003055TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010983DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003020SQ DCD003054TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010981DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003026SQ DCD003037TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010978DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003039SQ DCD003034TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010973DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003042SQ DCD003033TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010976DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002649AA DCD014025BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003018SQ DCD003063TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011007DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003011SQ DCD003061TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011006DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003035SQ DCD003060TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011004DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003043SQ DCD003044TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010995DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003040SQ DCD003043TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010998DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003037SQ DCD003042TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010999DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003010SQ DCD003041TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011001DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003019SQ DCD003040TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010991DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003023SQ DCD003039TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD010994DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002652AA DCD014026BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002998SQ DCD003051TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011010DT: FASTQ
DCD011105DT: BIGWIG GRCz10/danRer10
DCD011106DT: BIGWIG GRCz10/danRer10
DCD011107DT: BIGWIG GRCz10/danRer10
DCD011108DT: BIGWIG GRCz10/danRer10
DCD011110DT: BIGWIG GRCz10/danRer10
DCD011112DT: BIGWIG GRCz10/danRer10
DCD011115DT: COOL GRCz10/danRer10
DCD017489DT: BIGWIG GRCz11/danRer11
DCD017490DT: BIGWIG GRCz11/danRer11
DCD017491DT: BIGWIG GRCz11/danRer11
DCD017492DT: BIGWIG GRCz11/danRer11
DCD017494DT: BIGWIG GRCz11/danRer11
DCD017495DT: BIGWIG GRCz11/danRer11
DCD017499DT: BIGWIG GRCz11/danRer11
DCD017537DT: BIGWIG GRCz11/danRer11
DCD017538DT: BIGWIG GRCz11/danRer11
DCD017539DT: BIGWIG GRCz11/danRer11
DCD017540DT: BIGWIG GRCz11/danRer11
DCD017543DT: BIGWIG GRCz11/danRer11
DCD017544DT: BIGWIG GRCz11/danRer11
DCD017547DT: COOL GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003000SQ DCD003050TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011011DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003004SQ DCD003049TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011014DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003009SQ DCD003048TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011015DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007252BS DCD000428SR whole organism de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute TU/TL 256-cell 2.3
Applied Assay ID Biosample Replicate Assay
DCD002655AA DCD014020BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003038SQ DCD003065TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011038DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003022SQ DCD003064TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 07/03/2018
DCD011039DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002653AA DCD014021BR Hi-C_de_Wit_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003008SQ DCD003032TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011034DT: FASTQ
DCD011111DT: BIGWIG GRCz10/danRer10
DCD011113DT: BIGWIG GRCz10/danRer10
DCD011114DT: BIGWIG GRCz10/danRer10
DCD011116DT: COOL GRCz10/danRer10
DCD011117DT: BIGWIG GRCz10/danRer10
DCD011118DT: BIGWIG GRCz10/danRer10
DCD011119DT: BIGWIG GRCz10/danRer10
DCD017496DT: BIGWIG GRCz11/danRer11
DCD017497DT: BIGWIG GRCz11/danRer11
DCD017498DT: BIGWIG GRCz11/danRer11
DCD017500DT: BIGWIG GRCz11/danRer11
DCD017501DT: BIGWIG GRCz11/danRer11
DCD017502DT: BIGWIG GRCz11/danRer11
DCD017503DT: COOL GRCz11/danRer11
DCD017542DT: BIGWIG GRCz11/danRer11
DCD017545DT: BIGWIG GRCz11/danRer11
DCD017546DT: BIGWIG GRCz11/danRer11
DCD017548DT: BIGWIG GRCz11/danRer11
DCD017549DT: BIGWIG GRCz11/danRer11
DCD017550DT: BIGWIG GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD003005SQ DCD003028TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 07/03/2018
DCD011035DT: FASTQ