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 Maximum Read Length Sequencing Date
DCD003028SQ DCD003067TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 57 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 Maximum Read Length Sequencing Date
DCD003006SQ DCD003053TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 07/03/2018
DCD010956DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003033SQ DCD003052TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 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 Maximum Read Length Sequencing Date
DCD003014SQ DCD003071TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010968DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003021SQ DCD003062TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010966DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003031SQ DCD003046TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010972DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003003SQ DCD003031TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 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 Maximum Read Length Sequencing Date
DCD003025SQ DCD003073TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010964DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003041SQ DCD003072TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 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 Maximum Read Length Sequencing Date
DCD003036SQ DCD003070TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010960DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003024SQ DCD003066TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 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 Maximum Read Length Sequencing Date
DCD003032SQ DCD003045TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 57 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 Maximum Read Length Sequencing Date
DCD003030SQ DCD003047TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011022DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003012SQ DCD003038TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011032DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003015SQ DCD003036TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011027DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003017SQ DCD003035TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011030DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003016SQ DCD003030TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011023DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003027SQ DCD003029TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 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 Maximum Read Length Sequencing Date
DCD002999SQ DCD003069TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 07/03/2018
DCD011019DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003013SQ DCD003068TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 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 Maximum Read Length Sequencing Date
DCD003029SQ DCD003059TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010980DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003034SQ DCD003058TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010989DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003007SQ DCD003057TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010987DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003001SQ DCD003056TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010986DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003002SQ DCD003055TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010983DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003020SQ DCD003054TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010981DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003026SQ DCD003037TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010978DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003039SQ DCD003034TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD010973DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003042SQ DCD003033TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 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 Maximum Read Length Sequencing Date
DCD003018SQ DCD003063TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD011007DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003011SQ DCD003061TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD011006DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003035SQ DCD003060TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD011004DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003043SQ DCD003044TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010995DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003040SQ DCD003043TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010998DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003037SQ DCD003042TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010999DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003010SQ DCD003041TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD011001DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003019SQ DCD003040TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 07/03/2018
DCD010991DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003023SQ DCD003039TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 63 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 Maximum Read Length Sequencing Date
DCD002998SQ DCD003051TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 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 Maximum Read Length Sequencing Date
DCD003000SQ DCD003050TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 07/03/2018
DCD011011DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003004SQ DCD003049TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 07/03/2018
DCD011014DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003009SQ DCD003048TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 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 Maximum Read Length Sequencing Date
DCD003038SQ DCD003065TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 07/03/2018
DCD011038DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD003022SQ DCD003064TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina HiSeq 2500 unstranded 71 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 Maximum Read Length Sequencing Date
DCD003008SQ DCD003032TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 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 Maximum Read Length Sequencing Date
DCD003005SQ DCD003028TR de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute Illumina NextSeq 500 Mid-Output unstranded 79 07/03/2018
DCD011035DT: FASTQ