Series Summary for DCD000374SR

RNA-seq, Ribo-seq and PAL-seq of 3 stages: Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution

Survey

10.1016/j.cell.2011.11.055

GSE32880

To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq data, to identify more than 550 distinct lincRNAs in zebrafish.

True

mickael.dong

Oct. 24, 2017, 4:45 a.m.

Nov. 7, 2018, 6:43 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD007025BS DCD000374SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research WT Prim-5 — — 24 —
Applied Assay ID Biosample Replicate Assay
DCD002012AA DCD013593BR ChIP-seq_Bartel_Lab_H3K4me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002371SQ DCD002383TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007927DT: FASTQ
DCD008914DT: BIGNARROWPEAK GRCz10/danRer10
DCD009009DT: BIGWIG GRCz10/danRer10
DCD016499DT: BED GRCz11/danRer11
DCD016500DT: BAM GRCz11/danRer11
DCD016502DT: BIGNARROWPEAK GRCz11/danRer11
DCD016503DT: BIGNARROWPEAK GRCz11/danRer11
DCD016504DT: BIGWIG GRCz11/danRer11
DCD016726DT: BED GRCz10/danRer10
DCD016727DT: BAM GRCz10/danRer10
DCD016728DT: BIGNARROWPEAK GRCz10/danRer10
DCD016729DT: BIGNARROWPEAK GRCz10/danRer10
DCD017136DT: BAM GRCz10/danRer10
DCD017138DT: BED GRCz10/danRer10
DCD017139DT: BIGNARROWPEAK GRCz10/danRer10
DCD017140DT: BIGNARROWPEAK GRCz10/danRer10
DCD017144DT: BIGWIG GRCz10/danRer10
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002370SQ DCD002382TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007926DT: FASTQ
DCD008918DT: BIGNARROWPEAK GRCz10/danRer10
DCD009005DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002013AA DCD013594BR ChIP-seq_Bartel_Lab_H3K36me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002372SQ DCD002384TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007928DT: FASTQ
DCD009006DT: BIGWIG GRCz10/danRer10
DCD016310DT: BAM GRCz11/danRer11
DCD016311DT: BIGNARROWPEAK GRCz11/danRer11
DCD016312DT: BIGNARROWPEAK GRCz11/danRer11
DCD016313DT: BED GRCz11/danRer11
DCD016314DT: BIGWIG GRCz11/danRer11
DCD016742DT: BED GRCz10/danRer10
DCD016743DT: BIGNARROWPEAK GRCz10/danRer10
DCD016744DT: BIGNARROWPEAK GRCz10/danRer10
DCD016745DT: BAM GRCz10/danRer10
DCD017156DT: BED GRCz10/danRer10
DCD017157DT: BAM GRCz10/danRer10
DCD017158DT: BIGNARROWPEAK GRCz10/danRer10
DCD017159DT: BIGNARROWPEAK GRCz10/danRer10
DCD017162DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002014AA DCD013595BR ChIP-seq_Bartel_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002374SQ DCD002386TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007930DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002373SQ DCD002385TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007929DT: FASTQ
DCD016991DT: BAM GRCz10/danRer10
DCD017021DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD002015AA DCD013596BR ChIP-seq_Bartel_Lab_input_control_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002375SQ DCD002387TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx — 12/22/2011
DCD007931DT: FASTQ
DCD016983DT: BAM GRCz10/danRer10
DCD017004DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD002016AA DCD013597BR RNA-seq_Bartel_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002377SQ DCD002389TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx forward 12/22/2011
DCD007933DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002376SQ DCD002388TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx forward 12/22/2011
DCD007932DT: FASTQ
Applied Assay ID Biosample Replicate Assay Controlled By
DCD002017AA DCD013598BR 3P-seq_Bartel_Lab_0004AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002378SQ DCD002390TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx — ✘ forward — 12/22/2011
DCD007934DT: FASTQ
DCD011443DT: BED GRCz11/danRer11
DCD011444DT: BAM GRCz11/danRer11
DCD011445DT: BIGBED GRCz11/danRer11
DCD011446DT: BIGWIG GRCz11/danRer11
DCD011448DT: BED GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007026BS DCD000374SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research WT Protruding-mouth 72
Applied Assay ID Biosample Replicate Assay
DCD002018AA DCD013599BR ChIP-seq_Bartel_Lab_H3K4me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002380SQ DCD002392TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007936DT: FASTQ
DCD008921DT: BIGNARROWPEAK GRCz10/danRer10
DCD009010DT: BIGWIG GRCz10/danRer10
DCD016592DT: BED GRCz11/danRer11
DCD016593DT: BAM GRCz11/danRer11
DCD016596DT: BIGNARROWPEAK GRCz11/danRer11
DCD016597DT: BIGNARROWPEAK GRCz11/danRer11
DCD016598DT: BIGWIG GRCz11/danRer11
DCD016818DT: BED GRCz10/danRer10
DCD016819DT: BAM GRCz10/danRer10
DCD016820DT: BIGNARROWPEAK GRCz10/danRer10
DCD016821DT: BIGNARROWPEAK GRCz10/danRer10
DCD017254DT: BIGNARROWPEAK GRCz10/danRer10
DCD017257DT: BED GRCz10/danRer10
DCD017259DT: BAM GRCz10/danRer10
DCD017260DT: BIGNARROWPEAK GRCz10/danRer10
DCD017261DT: BIGWIG GRCz10/danRer10
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002379SQ DCD002391TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007935DT: FASTQ
DCD008915DT: BIGNARROWPEAK GRCz10/danRer10
DCD009008DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002019AA DCD013600BR ChIP-seq_Bartel_Lab_H3K36me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002381SQ DCD002393TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007937DT: FASTQ
DCD008913DT: BIGWIG GRCz10/danRer10
DCD016428DT: BAM GRCz11/danRer11
DCD016430DT: BED GRCz11/danRer11
DCD016431DT: BIGNARROWPEAK GRCz11/danRer11
DCD016432DT: BIGNARROWPEAK GRCz11/danRer11
DCD016436DT: BIGWIG GRCz11/danRer11
DCD016957DT: BED GRCz10/danRer10
DCD016958DT: BAM GRCz10/danRer10
DCD016959DT: BIGNARROWPEAK GRCz10/danRer10
DCD016960DT: BIGNARROWPEAK GRCz10/danRer10
DCD017427DT: BIGNARROWPEAK GRCz10/danRer10
DCD017428DT: BED GRCz10/danRer10
DCD017430DT: BAM GRCz10/danRer10
DCD017431DT: BIGNARROWPEAK GRCz10/danRer10
DCD017432DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002020AA DCD013601BR ChIP-seq_Bartel_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002383SQ DCD002395TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007939DT: FASTQ
DCD016996DT: BAM GRCz10/danRer10
DCD017016DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002382SQ DCD002394TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007938DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002021AA DCD013602BR ChIP-seq_Bartel_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002384SQ DCD002396TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007940DT: FASTQ
DCD016970DT: BAM GRCz10/danRer10
DCD017022DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD002022AA DCD013603BR RNA-seq_Bartel_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002386SQ DCD002398TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007942DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002385SQ DCD002397TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007941DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002023AA DCD013604BR 3P-seq_Bartel_Lab_0004AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002387SQ DCD002399TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007943DT: FASTQ
DCD011447DT: BAM GRCz11/danRer11
DCD011449DT: BIGBED GRCz11/danRer11
DCD011450DT: BED GRCz11/danRer11
DCD011451DT: BIGWIG GRCz11/danRer11
DCD011453DT: BED GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007027BS DCD000374SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research WT 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002024AA DCD013605BR ChIP-seq_Bartel_Lab_H3K4me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002388SQ DCD002400TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007944DT: FASTQ
DCD008919DT: BIGNARROWPEAK GRCz10/danRer10
DCD009007DT: BIGWIG GRCz10/danRer10
DCD016528DT: BED GRCz11/danRer11
DCD016529DT: BAM GRCz11/danRer11
DCD016531DT: BIGNARROWPEAK GRCz11/danRer11
DCD016532DT: BIGNARROWPEAK GRCz11/danRer11
DCD016533DT: BIGWIG GRCz11/danRer11
DCD016714DT: BIGNARROWPEAK GRCz10/danRer10
DCD016715DT: BED GRCz10/danRer10
DCD016716DT: BIGNARROWPEAK GRCz10/danRer10
DCD016717DT: BAM GRCz10/danRer10
DCD017121DT: BIGNARROWPEAK GRCz10/danRer10
DCD017122DT: BIGNARROWPEAK GRCz10/danRer10
DCD017123DT: BED GRCz10/danRer10
DCD017124DT: BIGWIG GRCz10/danRer10
DCD017125DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002025AA DCD013606BR ChIP-seq_Bartel_Lab_H3K36me3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002389SQ DCD002401TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007945DT: FASTQ
DCD008912DT: BIGWIG GRCz10/danRer10
DCD016580DT: BAM GRCz11/danRer11
DCD016582DT: BED GRCz11/danRer11
DCD016583DT: BIGNARROWPEAK GRCz11/danRer11
DCD016584DT: BIGNARROWPEAK GRCz11/danRer11
DCD016585DT: BIGWIG GRCz11/danRer11
DCD016878DT: BED GRCz10/danRer10
DCD016879DT: BAM GRCz10/danRer10
DCD016880DT: BIGNARROWPEAK GRCz10/danRer10
DCD016881DT: BIGNARROWPEAK GRCz10/danRer10
DCD017331DT: BIGNARROWPEAK GRCz10/danRer10
DCD017332DT: BED GRCz10/danRer10
DCD017334DT: BAM GRCz10/danRer10
DCD017335DT: BIGNARROWPEAK GRCz10/danRer10
DCD017336DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002026AA DCD013607BR ChIP-seq_Bartel_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002390SQ DCD002402TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007946DT: FASTQ
DCD016990DT: BAM GRCz10/danRer10
DCD017025DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD002027AA DCD013608BR 3P-seq_Bartel_Lab_0004AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002391SQ DCD002403TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx 12/22/2011
DCD007947DT: FASTQ
DCD011452DT: BAM GRCz11/danRer11
DCD011454DT: BED GRCz11/danRer11
DCD011455DT: BIGBED GRCz11/danRer11
DCD011456DT: BED GRCz11/danRer11
DCD011457DT: BIGWIG GRCz11/danRer11