Series Summary for DCD000370SR

RNA-seq, Ribo-seq and PAL-seq of 3 stages: Poly(A)-tail profiling reveals an embryonic switch in translational control

Case Control

10.1038/nature13007

GSE52809

Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails.

True

mickael.dong

Oct. 9, 2017, 8:36 a.m.

March 12, 2018, 3:49 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007002BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB 64-cell 2
Applied Assay ID Biosample Replicate Assay
DCD001979AA DCD013550BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002337SQ DCD002349TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007893DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001978AA DCD013551BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002336SQ DCD002348TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007892DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001977AA DCD013552BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002335SQ DCD002347TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007891DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007003BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Sphere 4
Applied Assay ID Biosample Replicate Assay
DCD001982AA DCD013547BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002340SQ DCD002352TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007896DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001981AA DCD013548BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002339SQ DCD002351TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007895DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001980AA DCD013549BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002338SQ DCD002350TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007894DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007004BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Shield — 6
Applied Assay ID Biosample Replicate Assay
DCD001985AA DCD013544BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002343SQ DCD002355TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007899DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001984AA DCD013545BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002342SQ DCD002354TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007898DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001983AA DCD013546BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002341SQ DCD002353TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007897DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD007005BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB 64-cell DCD007002BS — miR-132 2 —
Applied Assay ID Biosample Replicate Assay
DCD001988AA DCD013541BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002346SQ DCD002358TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007902DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001987AA DCD013542BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002345SQ DCD002357TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007901DT: FASTQ
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001986AA DCD013543BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002344SQ DCD002356TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 — ✘ unstranded — 01/09/2014
DCD007900DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007006BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB 64-cell DCD007002BS miR-155 2
Applied Assay ID Biosample Replicate Assay
DCD001991AA DCD013538BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002349SQ DCD002361TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007905DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001990AA DCD013539BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002348SQ DCD002360TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007904DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001989AA DCD013540BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002347SQ DCD002359TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007903DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007007BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Sphere DCD007003BS miR-132 4
Applied Assay ID Biosample Replicate Assay
DCD001994AA DCD013535BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002352SQ DCD002364TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007908DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001993AA DCD013536BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002351SQ DCD002363TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007907DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001992AA DCD013537BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002350SQ DCD002362TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007906DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007008BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Sphere DCD007003BS miR-155 4
Applied Assay ID Biosample Replicate Assay
DCD001997AA DCD013532BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002355SQ DCD002367TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007911DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001996AA DCD013533BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002354SQ DCD002366TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007910DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001995AA DCD013534BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002353SQ DCD002365TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007909DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007009BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Shield DCD007004BS miR-132 6
Applied Assay ID Biosample Replicate Assay
DCD002000AA DCD013529BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002358SQ DCD002370TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007914DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001999AA DCD013530BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002357SQ DCD002369TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007913DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001998AA DCD013531BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002356SQ DCD002368TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007912DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Treatment Hours Post Fertilization
DCD007010BS DCD000370SR whole organism Bartel Lab, Whitehead Institute for Biomedical Research AB Shield DCD007004BS miR-155 6
Applied Assay ID Biosample Replicate Assay
DCD002003AA DCD013526BR PAL-seq_Bartel_Lab_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002361SQ DCD002373TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina GAIIx unstranded 01/09/2014
DCD007917DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002002AA DCD013527BR Ribo-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002360SQ DCD002372TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007916DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002001AA DCD013528BR miRNA-seq_Bartel_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002359SQ DCD002371TR Bartel Lab, Whitehead Institute for Biomedical Research Illumina HiSeq 2000 unstranded 01/09/2014
DCD007915DT: FASTQ