DANIO-CODE DCC

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

Series type: Case Control

Publication: 10.1038/nature13007

GEO/SRA ID: GSE52809

Description: 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.

Is public: True

Added by User: mickael.dong

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

Series Last Edited: March 12, 2018, 3:49 a.m.

Assays

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	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	Hours Post Fertilization
DCD007005BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	64-cell	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
DCD001986AA	DCD013543BR	miRNA-seq_Bartel_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	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	Hours Post Fertilization
DCD007006BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	64-cell	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	Hours Post Fertilization
DCD007007BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	Sphere	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	Hours Post Fertilization
DCD007008BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	Sphere	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	Hours Post Fertilization
DCD007009BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	Shield	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	Hours Post Fertilization
DCD007010BS	DCD000370SR	whole organism	Bartel Lab, Whitehead Institute for Biomedical Research	AB	Shield	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

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

Assays

PAL-seq

Ribo-seq

miRNA-seq