DANIO-CODE DCC

Series Summary for DCD000138SR

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.

Series type: Survey

Publication: 10.1002/embj.201488411

GEO/SRA ID: GSE53693

Description: Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.

Is public: True

Added by User: giraldezlab

Date Added: May 6, 2016, 9:36 a.m.

Series Last Edited: Aug. 8, 2018, 6:08 a.m.

Assays

RNA-seq

RNA-seq_Giraldez_Lab_0002AS

Ribo-seq

Ribo-seq_Giraldez_Lab_0001AS

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006184BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	Prim-5	24

Applied Assay ID	Biosample Replicate	Assay
DCD000917AA	DCD012280BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000685SQ	DCD000857TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	03/25/2013

DCD000446DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000686SQ	DCD000857TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000445DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006200BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	30%-epiboly	5

Applied Assay ID	Biosample Replicate	Assay
DCD000849AA	DCD012296BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000698SQ	DCD000873TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000465DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000713SQ	DCD000873TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	08/17/2012

DCD000467DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000717SQ	DCD000873TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	01/15/2013

DCD000466DT: FASTQ

Applied Assay ID	Biosample Replicate	Assay
DCD000870AA	DCD012317BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000735SQ	DCD000894TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	08/17/2012

DCD000464DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000774SQ	DCD000894TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	01/15/2013

DCD000463DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000775SQ	DCD000894TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000462DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006206BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	Prim-5	24

Applied Assay ID	Biosample Replicate	Assay
DCD000855AA	DCD012302BR	RNA-seq_Giraldez_Lab_0002AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000758SQ	DCD000879TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	02/05/2013

DCD000453DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000759SQ	DCD000879TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000452DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006211BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	5-9 somites	12

Applied Assay ID	Biosample Replicate	Assay
DCD000860AA	DCD012307BR	RNA-seq_Giraldez_Lab_0002AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000692SQ	DCD000884TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000454DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000693SQ	DCD000884TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	02/05/2013

DCD000455DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006214BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	Long-pec	48

Applied Assay ID	Biosample Replicate	Assay
DCD000863AA	DCD012310BR	RNA-seq_Giraldez_Lab_0002AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000795SQ	DCD000887TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	02/05/2013

DCD000451DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000796SQ	DCD000887TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/23/2013

DCD000450DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006215BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	30%-epiboly	5

Applied Assay ID	Biosample Replicate	Assay
DCD000864AA	DCD012311BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000805SQ	DCD000888TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	08/17/2012

DCD000461DT: FASTQ

Applied Assay ID	Biosample Replicate	Assay
DCD000867AA	DCD012314BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000800SQ	DCD000891TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	08/17/2012

DCD000460DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006216BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	64-cell	2

Applied Assay ID	Biosample Replicate	Assay
DCD000865AA	DCD012312BR	Ribo-seq_Giraldez_Lab_0001AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000665SQ	DCD000889TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	03/25/2013

DCD000442DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000689SQ	DCD000889TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/23/2013

DCD000440DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000690SQ	DCD000889TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000441DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000694SQ	DCD000889TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/23/2013

DCD000439DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Treatment	Hours Post Fertilization
DCD006222BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	30%-epiboly	—	5

Applied Assay ID	Biosample Replicate	Assay	Controlled By
DCD000871AA	DCD012318BR	RNA-seq_Giraldez_Lab_0002AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000658SQ	DCD000895TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/23/2013

DCD000458DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000750SQ	DCD000895TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	08/17/2012

DCD000459DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Treatment	Hours Post Fertilization
DCD006232BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	5-9 somites	cyclohex	12

Applied Assay ID	Biosample Replicate	Assay	Controlled By
DCD000852AA	DCD012299BR	Ribo-seq_Giraldez_Lab_0001AS	DCD000860AA

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000761SQ	DCD000876TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000447DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000763SQ	DCD000876TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	03/25/2013

DCD000448DT: FASTQ

Applied Assay ID	Biosample Replicate	Assay	Controlled By
DCD000881AA	DCD012328BR	Ribo-seq_Giraldez_Lab_0001AS	DCD000860AA

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000724SQ	DCD000905TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	03/12/2013

DCD000449DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Hours Post Fertilization
DCD006254BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	64-cell	2

Applied Assay ID	Biosample Replicate	Assay
DCD000903AA	DCD012350BR	RNA-seq_Giraldez_Lab_0002AS

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000734SQ	DCD000927TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000456DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000753SQ	DCD000927TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	forward	76	02/05/2013

DCD000457DT: FASTQ

Biosample ID	Series	biosample_type	biosample_lab	genetic_background	stage	Controlled By	anatomical_term	Treatment	Hours Post Fertilization	Mutation Description
DCD006261BS	DCD000138SR	whole organism	Giraldez Lab, Yale	AB/TU	Long-pec		—	cyclohex	48	—

Applied Assay ID	Biosample Replicate	Assay	Controlled By
DCD000910AA	DCD012357BR	Ribo-seq_Giraldez_Lab_0001AS	DCD000863AA

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Strand	Maximum Read Length	Sequencing Date
DCD000725SQ	DCD000934TR	Giraldez Lab, Yale	Illumina	HiSeq 2000	forward	76	04/05/2013

DCD000443DT: FASTQ

Sequencing ID	Technical Replicate	Sequencing Lab	Platform	Instrument	Chemistry Version	Paired End	Strand	Maximum Read Length	Sequencing Date
DCD000730SQ	DCD000934TR	Giraldez Lab, Yale	Illumina	HiSeq 2500	—	✘	forward	76	03/25/2013

DCD000444DT: FASTQ