metadata: run_metadata: 2,195 rows where devstage_curation = "Gastrula" and tissue

2,195 rows where devstage_curation = "Gastrula" and tissue_curation = "Undetermined"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9717	9717	ERR3842002	ERX3854564	ERS4268611	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4Ei	SAMEA6504165	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:05:06Z\|ENA LAST UPDATE:2020 01 27T16:04:35Z\|External Id:SAMEA6504165\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:05:06Z\|INSDC last update:2020 01 27T16:04:35Z\|INSDC status:public\|Submitter Id:Shield 4Ei\|common name:zebrafish\|sample name:Shield 4Ei\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 2	Shield 4Ei LSU	OTHER	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			10915827408.0	143629308.0	ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 2	0:76	A:3900515347;C:2409375725;G:3041696977;T:1564127293;N:112066	76		3900515347	2409375725	3041696977	1564127293	112066	ERX3854564	ERS4268611	ERA2359340	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.64398		0.40944		0.98817		0.59337		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9718	9718	ERR3842001	ERX3854563	ERS4268611	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4Ei	SAMEA6504165	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:05:06Z\|ENA LAST UPDATE:2020 01 27T16:04:35Z\|External Id:SAMEA6504165\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:05:06Z\|INSDC last update:2020 01 27T16:04:35Z\|INSDC status:public\|Submitter Id:Shield 4Ei\|common name:zebrafish\|sample name:Shield 4Ei\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 1	Shield 4Ei SSU	OTHER	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			7154041880.0	94132130.0	ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 1	0:76	A:2939474250;C:1489083073;G:1922522149;T:802890185;N:72223	76		2939474250	1489083073	1922522149	802890185	72223	ERX3854563	ERS4268611	ERA2359340	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.4369		0.25417		0.9867		0.60047		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9719	9719	ERR3842000	ERX3854562	ERS4268611	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4Ei	SAMEA6504165	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:05:06Z\|ENA LAST UPDATE:2020 01 27T16:04:35Z\|External Id:SAMEA6504165\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:05:06Z\|INSDC last update:2020 01 27T16:04:35Z\|INSDC status:public\|Submitter Id:Shield 4Ei\|common name:zebrafish\|sample name:Shield 4Ei\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 10	Shield 4Ei	OTHER	RNA Seq	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			1435748376.0	18891426.0	ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 10	0:76	A:489056518;C:372290023;G:393663734;T:180723629;N:14472	76		489056518	372290023	393663734	180723629	14472	ERX3854562	ERS4268611	ERA2359305	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.11942		0.03394		0.98971		0.62271		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9720	9720	ERR3841999	ERX3854561	ERS3556006	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 3	SAMEA5752547	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752547\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:10\|common name:zebrafish\|dev stage:Shield\|sample name:10\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 9	Shield 3	OTHER	RNA Seq	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			1168482976.0	15374776.0	ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 9	0:76	A:516070340;C:238363428;G:268806793;T:145231087;N:11328	76		516070340	238363428	268806793	145231087	11328	ERX3854561	ERS3556006	ERA2359305	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.22586		0.10275		0.97281		0.47683		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9721	9721	ERR3841998	ERX3854560	ERS3556007	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4150NT	SAMEA5752548	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752548\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:11\|common name:zebrafish\|dev stage:Shield\|sample name:11\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 8	Shield 150NT	OTHER	RNA Seq	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			1188343980.0	15636105.0	ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 8	0:76	A:580658556;C:223116826;G:260847322;T:123709681;N:11595	76		580658556	223116826	260847322	123709681	11595	ERX3854560	ERS3556007	ERA2359305	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.27037		0.13972		0.97392		0.39459		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9722	9722	ERR3841997	ERX3854559	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 7	Shield 1	OTHER	RNA Seq	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2020 02 14			1278891444.0	16827519.0	ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 7	0:76	A:571738369;C:256385478;G:295145281;T:155610082;N:12234	76		571738369	256385478	295145281	155610082	12234	ERX3854559	ERS3556004	ERA2359305	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.23116		0.11137		0.97932		0.45978		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9729	9729	ERR3489881	ERX3511296	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 33	Shield 1 F20	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			975578636.0	12836561.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 33	0:76	A:398325549;C:237563934;G:230721299;T:108957698;N:10156	76		398325549	237563934	230721299	108957698	10156	ERX3511296	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.33102		0.19766		0.99918		0.12812		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9730	9730	ERR3489880	ERX3511295	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 32	Shield 1 F19	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			931166668.0	12252193.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 32	0:76	A:271081669;C:253947035;G:272354427;T:133774815;N:8722	76		271081669	253947035	272354427	133774815	8722	ERX3511295	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.15598		0.10707		0.99902		0.47314		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9731	9731	ERR3489879	ERX3511294	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 31	Shield 1 F18	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1506513268.0	19822543.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 31	0:76	A:493273515;C:456544968;G:391677033;T:165002559;N:15193	76		493273515	456544968	391677033	165002559	15193	ERX3511294	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.01562		0.0053		0.99908		0.8127		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9732	9732	ERR3489878	ERX3511293	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 30	Shield 1 F17	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1259456496.0	16571796.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 30	0:76	A:471473123;C:333726472;G:302016190;T:152228002;N:12709	76		471473123	333726472	302016190	152228002	12709	ERX3511293	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.18339		0.12544		0.99928		0.22368		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9733	9733	ERR3489877	ERX3511292	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 29	Shield 1 F16	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1364615872.0	17955472.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 29	0:76	A:539462776;C:341141880;G:314571683;T:169426048;N:13485	76		539462776	341141880	314571683	169426048	13485	ERX3511292	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.11663		0.07319		0.99939		0.25377		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9734	9734	ERR3489876	ERX3511291	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 28	Shield 1 F15	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			952605888.0	12534288.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 28	0:76	A:414133320;C:219437277;G:207418049;T:111607418;N:9824	76		414133320	219437277	207418049	111607418	9824	ERX3511291	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.17603		0.10972		0.99935		0.13311		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9735	9735	ERR3489875	ERX3511290	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 27	Shield 1 F14	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			870952628.0	11459903.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 27	0:76	A:357710338;C:221475453;G:191231014;T:100526675;N:9148	76		357710338	221475453	191231014	100526675	9148	ERX3511290	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.1248		0.06422		0.99896		0.34819		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9736	9736	ERR3489874	ERX3511289	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 26	Shield 1 F13	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			981672620.0	12916745.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 26	0:76	A:434153198;C:223317075;G:198260771;T:125932145;N:9431	76		434153198	223317075	198260771	125932145	9431	ERX3511289	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.44603		0.25602		0.99874		0.18074		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9737	9737	ERR3489873	ERX3511288	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 25	Shield 1 F12	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1304618128.0	17166028.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 25	0:76	A:651341516;C:270458496;G:243929520;T:138874830;N:13766	76		651341516	270458496	243929520	138874830	13766	ERX3511288	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.64293		0.38159		0.99886		0.07313		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9738	9738	ERR3489872	ERX3511287	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 24	Shield 1 F10	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1336115948.0	17580473.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 24	0:76	A:608634206;C:295943144;G:286494431;T:145029697;N:14470	76		608634206	295943144	286494431	145029697	14470	ERX3511287	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.68758		0.47517		0.99898		0.02301		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9739	9739	ERR3489871	ERX3511286	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 23	Shield 1 F9	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			1434402492.0	18873717.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 23	0:76	A:658705664;C:297967081;G:295595736;T:182118632;N:15379	76		658705664	297967081	295595736	182118632	15379	ERX3511286	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.74246		0.44235		0.99701		0.03112		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9740	9740	ERR3489870	ERX3511285	ERS3556007	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4150NT	SAMEA5752548	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752548\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:11\|common name:zebrafish\|dev stage:Shield\|sample name:11\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 22	Shield 4150NT LSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 24			24063208094.0	159358994.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 22	0:151	A:7153064588;C:5242791119;G:8513736630;T:3152547276;N:1068481	151		7153064588	5242791119	8513736630	3152547276	1068481	ERX3511285	ERS3556007	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.81267		0.27138		0.99868		0.91938		151		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9741	9741	ERR3489869	ERX3511284	ERS3556007	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 4150NT	SAMEA5752548	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752548\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:11\|common name:zebrafish\|dev stage:Shield\|sample name:11\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 21	Shield 4150NT SSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 24			14987998619.0	99258269.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 21	0:151	A:4578051806;C:2616328922;G:5914185813;T:1878780090;N:651988	151		4578051806	2616328922	5914185813	1878780090	651988	ERX3511284	ERS3556007	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.77096		0.5278		0.99833		0.42635		151		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9746	9746	ERR3489864	ERX3511279	ERS3556006	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 3	SAMEA5752547	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752547\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:10\|common name:zebrafish\|dev stage:Shield\|sample name:10\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 16	Shield 3 LSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			11777220072.0	154963422.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 16	0:76	A:3368038444;C:3190496935;G:3529701152;T:1688766119;N:217422	76		3368038444	3190496935	3529701152	1688766119	217422	ERX3511279	ERS3556006	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.70681		0.18846		0.99332		0.71978		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9747	9747	ERR3489863	ERX3511278	ERS3556006	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 3	SAMEA5752547	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752547\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:10\|common name:zebrafish\|dev stage:Shield\|sample name:10\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 15	Shield 3 SSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			7920419952.0	104216052.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 15	0:76	A:2990167185;C:1767708808;G:2104830363;T:1057568560;N:145036	76		2990167185	1767708808	2104830363	1057568560	145036	ERX3511278	ERS3556006	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.5052		0.30841		0.99129		0.60948		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9748	9748	ERR3489862	ERX3511277	ERS3556005	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 2	SAMEA5752546	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752546\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:9\|common name:zebrafish\|dev stage:Shield\|sample name:9\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 14	Shield 2 LSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			9775297004.0	128622329.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 14	0:76	A:4750565405;C:2540992255;G:1698817649;T:784832634;N:89061	76		4750565405	2540992255	1698817649	784832634	89061	ERX3511277	ERS3556005	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.74003		0.5616		0.99855		0.03607		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9749	9749	ERR3489861	ERX3511276	ERS3556005	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 2	SAMEA5752546	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752546\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:9\|common name:zebrafish\|dev stage:Shield\|sample name:9\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 13	Shield 2 SSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			8210103300.0	108027675.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 13	0:76	A:3300825043;C:2576709678;G:1707115198;T:625376255;N:77126	76		3300825043	2576709678	1707115198	625376255	77126	ERX3511276	ERS3556005	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.2787		0.17583		0.99752		0.50171		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9750	9750	ERR3489860	ERX3511275	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 12	Shield 1 LSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			2437679936.0	32074736.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 12	0:76	A:764355184;C:710492003;G:664031460;T:298777374;N:23915	76		764355184	710492003	664031460	298777374	23915	ERX3511275	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.0406		0.02417		0.99908		0.61299		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
9751	9751	ERR3489859	ERX3511274	ERS3556004	ERP116106	PRJEB33323	Deconstructing the individual steps of vertebrate translation initiation	ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422	Other	In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 07 03	Shield 1	SAMEA5752545	Computational Biology Unit	ENA FIRST PUBLIC:2020 03 27T17:04:59Z\|ENA LAST UPDATE:2019 07 03T10:01:14Z\|External Id:SAMEA5752545\|INSDC center name:Computational Biology Unit\|INSDC first public:2020 03 27T17:04:59Z\|INSDC last update:2019 07 03T10:01:14Z\|INSDC status:public\|Submitter Id:8\|common name:zebrafish\|dev stage:Shield\|sample name:8\|scientific name:Danio rerio	NextSeq 500 sequencing	ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 11	Shield 1 SSU	None	RCP seq	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	ERP116106	NextSeq 500 sequencing	ENA FIRST PUBLIC:2020 03 27\|ENA LAST UPDATE:2019 08 22			3157243376.0	41542676.0	ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 11	0:76	A:1443205052;C:715251024;G:633421305;T:365333650;N:32345	76		1443205052	715251024	633421305	365333650	32345	ERX3511274	ERS3556004	ERA2100634	Computational Biology Unit\|European Nucleotide Archive	Computational Biology Unit	1	0.47643		0.27944		0.99896		0.11464		76		B		usable mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	Unknown	2019-07-03	Gastrula	Embryo	Undetermined	Embryo Imprecise
22297	22297	ERR959156	ERX1036203	ERS790174	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482770	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482770\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 83 sc 1963356\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GCTCCTTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 83 sc 1963356\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#83	10362876	Illumina sequencing of library 10362876 constructed from sample accession ERS790174 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GCTCCTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#83.cram	cram	81251300.0	625010.0	SC RUN 13080 2#83	0:55 1:75	A:22686562;C:15358120;G:14210136;T:28968512;N:27970	55	75	22686562	15358120	14210136	28968512	27970	ERX1036203	ERS790174	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.39171	0.99447	0.39135	0.77891	0.99987	0.99596	0.1923	0.04331	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22298	22298	ERR959155	ERX1036202	ERS790173	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482769	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482769\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 82 sc 1963355\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GAGCCAAT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 82 sc 1963355\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#82	10362875	Illumina sequencing of library 10362875 constructed from sample accession ERS790173 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GAGCCAAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#82.cram	cram	32607250.0	250825.0	SC RUN 13080 2#82	0:55 1:75	A:7500490;C:7924976;G:5795737;T:11374701;N:11346	55	75	7500490	7924976	5795737	11374701	11346	ERX1036202	ERS790173	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.50926	0.7335	0.50562	0.73278	0.99993	0.99801	0.96644	0.43902	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22299	22299	ERR959154	ERX1036201	ERS790172	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482768	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:28:39Z\|External Id:SAMEA3482768\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:28:39Z\|INSDC status:public\|Submitter Id:shield cell 81 sc 1963354\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GGAATGAT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 81 sc 1963354\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#81	10362874	Illumina sequencing of library 10362874 constructed from sample accession ERS790172 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GGAATGAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#81.cram	cram	51847510.0	398827.0	SC RUN 13080 2#81	0:55 1:75	A:13642764;C:8498883;G:8892127;T:20794619;N:19117	55	75	13642764	8498883	8892127	20794619	19117	ERX1036201	ERS790172	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.43316	0.80682	0.43245	0.55718	0.99987	0.9974	0.6375	0.49253	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22300	22300	ERR959153	ERX1036200	ERS790171	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482767	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482767\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 80 sc 1963353\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GTCGCTAT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 80 sc 1963353\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#80	10362873	Illumina sequencing of library 10362873 constructed from sample accession ERS790171 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GTCGCTAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#80.cram	cram	442673920.0	3405184.0	SC RUN 13080 2#80	0:55 1:75	A:107160617;C:76661084;G:81632399;T:177053991;N:165829	55	75	107160617	76661084	81632399	177053991	165829	ERX1036200	ERS790171	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.35142	0.83662	0.3481	0.23165	0.99967	0.99602	0.69653	0.5302	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22301	22301	ERR959152	ERX1036199	ERS790170	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482766	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:42:57Z\|External Id:SAMEA3482766\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:42:57Z\|INSDC status:public\|Submitter Id:shield cell 79 sc 1963352\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GTTAGCCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 79 sc 1963352\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#79	10362872	Illumina sequencing of library 10362872 constructed from sample accession ERS790170 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GTTAGCCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#79.cram	cram	293606170.0	2258509.0	SC RUN 13080 2#79	0:55 1:75	A:65939139;C:58873446;G:58131977;T:110550725;N:110883	55	75	65939139	58873446	58131977	110550725	110883	ERX1036199	ERS790170	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.2836	0.40872	0.28092	0.11688	0.99967	0.99679	0.66666	0.48475	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22302	22302	ERR959151	ERX1036198	ERS790169	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482765	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:28:39Z\|External Id:SAMEA3482765\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:28:39Z\|INSDC status:public\|Submitter Id:shield cell 78 sc 1963351\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GCATGGCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 78 sc 1963351\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#78	10362871	Illumina sequencing of library 10362871 constructed from sample accession ERS790169 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GCATGGCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#78.cram	cram	140251020.0	1078854.0	SC RUN 13080 2#78	0:55 1:75	A:31075420;C:25777335;G:25496619;T:57853020;N:48626	55	75	31075420	25777335	25496619	57853020	48626	ERX1036198	ERS790169	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.44526	0.91664	0.40548	0.29201	0.99973	0.99502	0.976	0.11356	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22303	22303	ERR959150	ERX1036197	ERS790168	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482764	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482764\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 77 sc 1963350\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GAGGTGCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 77 sc 1963350\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#77	10362870	Illumina sequencing of library 10362870 constructed from sample accession ERS790168 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GAGGTGCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#77.cram	cram	73287890.0	563753.0	SC RUN 13080 2#77	0:55 1:75	A:18107993;C:11894556;G:12406456;T:30852895;N:25990	55	75	18107993	11894556	12406456	30852895	25990	ERX1036197	ERS790168	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.15875	0.89451	0.15799	0.038	0.99979	0.99444	0.44303	0.11534	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22304	22304	ERR959149	ERX1036196	ERS790167	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482763	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482763\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 76 sc 1963349\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GTACATCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 76 sc 1963349\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#76	10362869	Illumina sequencing of library 10362869 constructed from sample accession ERS790167 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GTACATCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#76.cram	cram	277079400.0	2131380.0	SC RUN 13080 2#76	0:55 1:75	A:65500394;C:58060011;G:52775015;T:100636311;N:107669	55	75	65500394	58060011	52775015	100636311	107669	ERX1036196	ERS790167	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.32152	0.613	0.31443	0.3473	0.99981	0.99782	0.86936	0.71869	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22305	22305	ERR959148	ERX1036195	ERS790166	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482762	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:28:39Z\|External Id:SAMEA3482762\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:28:39Z\|INSDC status:public\|Submitter Id:shield cell 75 sc 1963348\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GAATCTGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 75 sc 1963348\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#75	10362868	Illumina sequencing of library 10362868 constructed from sample accession ERS790166 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GAATCTGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#75.cram	cram	928786950.0	7144515.0	SC RUN 13080 2#75	0:55 1:75	A:226622517;C:150322025;G:157654677;T:393861929;N:325802	55	75	226622517	150322025	157654677	393861929	325802	ERX1036195	ERS790166	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.29201	0.87845	0.27969	0.14381	0.99943	0.99397	0.49369	0.41778	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22306	22306	ERR959147	ERX1036194	ERS790165	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482761	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482761\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 74 sc 1963347\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GGTCGTGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 74 sc 1963347\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#74	10362867	Illumina sequencing of library 10362867 constructed from sample accession ERS790165 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GGTCGTGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#74.cram	cram	34256040.0	263508.0	SC RUN 13080 2#74	0:55 1:75	A:7812964;C:4765758;G:5526797;T:16139059;N:11462	55	75	7812964	4765758	5526797	16139059	11462	ERX1036194	ERS790165	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.34629	0.99846	0.34563	0.00261	0.99983	0.99604	0.25	0.37345	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22307	22307	ERR959146	ERX1036193	ERS790164	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482760	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:42:57Z\|External Id:SAMEA3482760\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:42:57Z\|INSDC status:public\|Submitter Id:shield cell 73 sc 1963346\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GCAACATT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 73 sc 1963346\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#73	10362866	Illumina sequencing of library 10362866 constructed from sample accession ERS790164 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GCAACATT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#73.cram	cram	85617610.0	658597.0	SC RUN 13080 2#73	0:55 1:75	A:20793000;C:17608067;G:18169033;T:29015717;N:31793	55	75	20793000	17608067	18169033	29015717	31793	ERX1036193	ERS790164	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.40764	0.3146	0.40698	0.31422	0.99993	0.99886	0.25	0.48387	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22308	22308	ERR959145	ERX1036192	ERS790163	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482759	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:28:39Z\|External Id:SAMEA3482759\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:28:39Z\|INSDC status:public\|Submitter Id:shield cell 72 sc 1963345\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GACGGATT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 72 sc 1963345\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#72	10362865	Illumina sequencing of library 10362865 constructed from sample accession ERS790163 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GACGGATT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#72.cram	cram	59492290.0	457633.0	SC RUN 13080 2#72	0:55 1:75	A:14758341;C:11714823;G:12785261;T:20211008;N:22857	55	75	14758341	11714823	12785261	20211008	22857	ERX1036192	ERS790163	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.47426	0.60775	0.47413	0.51001	0.99993	0.99945	0.0	0.99939	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22309	22309	ERR959144	ERX1036191	ERS790162	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482758	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T01:59:34Z\|External Id:SAMEA3482758\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T01:59:34Z\|INSDC status:public\|Submitter Id:shield cell 71 sc 1963344\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GTGTCCTT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 71 sc 1963344\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#71	10362864	Illumina sequencing of library 10362864 constructed from sample accession ERS790162 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GTGTCCTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#71.cram	cram	119173730.0	916721.0	SC RUN 13080 2#71	0:55 1:75	A:29451975;C:26610085;G:22832152;T:40234545;N:44973	55	75	29451975	26610085	22832152	40234545	44973	ERX1036191	ERS790162	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.32348	0.71219	0.31887	0.57568	0.99987	0.99896	0.01204	0.00125	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22310	22310	ERR959130	ERX1036177	ERS790148	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482744	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:27:21Z\|External Id:SAMEA3482744\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:27:21Z\|INSDC status:public\|Submitter Id:shield cell 57 sc 1963330\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCTACGAC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 57 sc 1963330\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#57	10362850	Illumina sequencing of library 10362850 constructed from sample accession ERS790148 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCTACGAC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#57.cram	cram	49591880.0	381476.0	SC RUN 13080 2#57	0:55 1:75	A:11297647;C:10202861;G:11417451;T:16654862;N:19059	55	75	11297647	10202861	11417451	16654862	19059	ERX1036177	ERS790148	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.06563	0.10159	0.06562	0.10145	1.0	0.99961		0.47619	55	75	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22311	22311	ERR959129	ERX1036176	ERS790147	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482743	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482743\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 56 sc 1963329\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTGCGTAC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 56 sc 1963329\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#56	10362849	Illumina sequencing of library 10362849 constructed from sample accession ERS790147 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTGCGTAC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#56.cram	cram	31516550.0	242435.0	SC RUN 13080 2#56	0:55 1:75	A:10186445;C:5121042;G:4601077;T:11596185;N:11801	55	75	10186445	5121042	4601077	11596185	11801	ERX1036176	ERS790147	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.41562	0.66811	0.41426	0.56647	0.99987	0.99088	0.54166	0.50229	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22312	22312	ERR959128	ERX1036175	ERS790146	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482742	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:42:56Z\|External Id:SAMEA3482742\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:42:56Z\|INSDC status:public\|Submitter Id:shield cell 55 sc 1963328\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTCGCACC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 55 sc 1963328\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#55	10362848	Illumina sequencing of library 10362848 constructed from sample accession ERS790146 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTCGCACC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#55.cram	cram	141272690.0	1086713.0	SC RUN 13080 2#55	0:55 1:75	A:32956117;C:30353092;G:26734703;T:51178716;N:50062	55	75	32956117	30353092	26734703	51178716	50062	ERX1036175	ERS790146	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.33506	0.73603	0.33283	0.51025	0.99985	0.99707	0.55494	0.11528	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22313	22313	ERR959127	ERX1036174	ERS790145	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482741	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:39Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482741\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:39Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 54 sc 1963327\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGTTCTCC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 54 sc 1963327\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#54	10362847	Illumina sequencing of library 10362847 constructed from sample accession ERS790145 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGTTCTCC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#54.cram	cram	51875200.0	399040.0	SC RUN 13080 2#54	0:55 1:75	A:13277711;C:10311958;G:9435214;T:18831879;N:18438	55	75	13277711	10311958	9435214	18831879	18438	ERX1036174	ERS790145	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.61678	0.89504	0.6167	0.8949	0.99991	0.99959	0.5	0.4	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22314	22314	ERR959126	ERX1036173	ERS790144	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482740	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482740\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 53 sc 1963326\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TACCGAGC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 53 sc 1963326\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#53	10362846	Illumina sequencing of library 10362846 constructed from sample accession ERS790144 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TACCGAGC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#53.cram	cram	98518680.0	757836.0	SC RUN 13080 2#53	0:55 1:75	A:24097345;C:19470948;G:20115699;T:34797377;N:37311	55	75	24097345	19470948	20115699	34797377	37311	ERX1036173	ERS790144	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.09178	0.12901	0.09122	0.09297	0.99993	0.99945	0.88235	0.99799	55	75	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22315	22315	ERR959125	ERX1036172	ERS790143	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482739	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482739\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 52 sc 1963325\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCGTTAGC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 52 sc 1963325\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#52	10362845	Illumina sequencing of library 10362845 constructed from sample accession ERS790143 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCGTTAGC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#52.cram	cram	170675050.0	1312885.0	SC RUN 13080 2#52	0:55 1:75	A:37755087;C:38276634;G:37744045;T:56834431;N:64853	55	75	37755087	38276634	37744045	56834431	64853	ERX1036172	ERS790143	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.37299	0.27233	0.37254	0.22951	0.99993	0.99701	0.16666	0.01443	55	75	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22316	22316	ERR959124	ERX1036171	ERS790142	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482738	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482738\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 51 sc 1963324\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTACTCGC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 51 sc 1963324\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#51	10362844	Illumina sequencing of library 10362844 constructed from sample accession ERS790142 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTACTCGC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#51.cram	cram	210207400.0	1616980.0	SC RUN 13080 2#51	0:55 1:75	A:53335077;C:44246750;G:41245337;T:71302463;N:77773	55	75	53335077	44246750	41245337	71302463	77773	ERX1036171	ERS790142	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.38978	0.49421	0.38958	0.39883	0.99993	0.99827	0.2	0.1154	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22317	22317	ERR959123	ERX1036170	ERS790141	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482737	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482737\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 50 sc 1963323\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TATGTGGC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 50 sc 1963323\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#50	10362843	Illumina sequencing of library 10362843 constructed from sample accession ERS790141 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TATGTGGC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#50.cram	cram	155379120.0	1195224.0	SC RUN 13080 2#50	0:55 1:75	A:36695444;C:30836149;G:30072179;T:57720020;N:55328	55	75	36695444	30836149	30072179	57720020	55328	ERX1036170	ERS790141	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.39524	0.9288	0.38256	0.46914	0.99977	0.99697	0.97209	0.50926	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22318	22318	ERR959122	ERX1036169	ERS790140	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482736	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:42:56Z\|External Id:SAMEA3482736\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:42:56Z\|INSDC status:public\|Submitter Id:shield cell 49 sc 1963322\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGTCTATC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 49 sc 1963322\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#49	10362842	Illumina sequencing of library 10362842 constructed from sample accession ERS790140 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGTCTATC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#49.cram	cram	102636560.0	789512.0	SC RUN 13080 2#49	0:55 1:75	A:22346887;C:21751856;G:20475807;T:38024041;N:37969	55	75	22346887	21751856	20475807	38024041	37969	ERX1036169	ERS790140	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.22946	0.3106	0.19779	0.0988	0.99989	0.99868	0.91361	0.18925	55	75	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22319	22319	ERR959121	ERX1036168	ERS790139	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482735	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482735\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 48 sc 1963321\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTCAGCTC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 48 sc 1963321\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#48	10362841	Illumina sequencing of library 10362841 constructed from sample accession ERS790139 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTCAGCTC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#48.cram	cram	266390540.0	2049158.0	SC RUN 13080 2#48	0:55 1:75	A:68745323;C:46075992;G:48621976;T:102852422;N:94827	55	75	68745323	46075992	48621976	102852422	94827	ERX1036168	ERS790139	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.27739	0.77629	0.24406	0.20438	0.99963	0.9959	0.01723	0.29969	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22320	22320	ERR959120	ERX1036167	ERS790138	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482734	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482734\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 47 sc 1963320\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TACTAGTC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 47 sc 1963320\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#47	10362840	Illumina sequencing of library 10362840 constructed from sample accession ERS790138 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TACTAGTC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#47.cram	cram	153030150.0	1177155.0	SC RUN 13080 2#47	0:55 1:75	A:39584099;C:31637881;G:28924812;T:52826929;N:56429	55	75	39584099	31637881	28924812	52826929	56429	ERX1036167	ERS790138	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.47789	0.59429	0.41226	0.41666	0.99975	0.99805	0.95964	0.9677	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22321	22321	ERR959119	ERX1036166	ERS790137	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482733	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482733\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 46 sc 1963319\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCAGATTC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 46 sc 1963319\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#46	10362839	Illumina sequencing of library 10362839 constructed from sample accession ERS790137 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCAGATTC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#46.cram	cram	53272830.0	409791.0	SC RUN 13080 2#46	0:55 1:75	A:13227428;C:10233837;G:10058716;T:19732728;N:20121	55	75	13227428	10233837	10058716	19732728	20121	ERX1036166	ERS790137	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.21517	0.68432	0.20407	0.21938	0.99989	0.99916	0.98883	0.13173	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22322	22322	ERR959118	ERX1036165	ERS790136	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482732	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482732\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 45 sc 1963318\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TATGCCAG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 45 sc 1963318\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#45	10362838	Illumina sequencing of library 10362838 constructed from sample accession ERS790136 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TATGCCAG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#45.cram	cram	277234360.0	2132572.0	SC RUN 13080 2#45	0:55 1:75	A:63312107;C:45992169;G:51562233;T:116267868;N:99983	55	75	63312107	45992169	51562233	116267868	99983	ERX1036165	ERS790136	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.38883	0.8082	0.38156	0.23008	0.99967	0.99261	0.75037	0.36339	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22323	22323	ERR959105	ERX1036152	ERS790123	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482719	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482719\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 32 sc 1963305\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 32 sc 1963305\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#32	10362825	Illumina sequencing of library 10362825 constructed from sample accession ERS790123 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTCCATTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#32.cram	cram	158290340.0	1217618.0	SC RUN 13080 2#32	0:55 1:75	A:37279764;C:30780704;G:28231667;T:61940512;N:57693	55	75	37279764	30780704	28231667	61940512	57693	ERX1036152	ERS790123	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.36545	0.74741	0.36457	0.39025	0.99985	0.99748	0.74285	0.39495	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22324	22324	ERR959104	ERX1036151	ERS790122	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482718	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:42:02Z\|External Id:SAMEA3482718\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:42:02Z\|INSDC status:public\|Submitter Id:shield cell 31 sc 1963304\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 31 sc 1963304\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#31	10362824	Illumina sequencing of library 10362824 constructed from sample accession ERS790122 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAGTCTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#31.cram	cram	151841950.0	1168015.0	SC RUN 13080 2#31	0:55 1:75	A:37631244;C:24385578;G:26308216;T:63459798;N:57114	55	75	37631244	24385578	26308216	63459798	57114	ERX1036151	ERS790122	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.2592	0.84623	0.25771	0.14805	0.99975	0.99575	0.125	0.34071	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22325	22325	ERR959103	ERX1036150	ERS790121	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482717	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:25:39Z\|External Id:SAMEA3482717\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:25:39Z\|INSDC status:public\|Submitter Id:shield cell 30 sc 1963303\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 30 sc 1963303\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#30	10362823	Illumina sequencing of library 10362823 constructed from sample accession ERS790121 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGTGGTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#30.cram	cram	73630960.0	566392.0	SC RUN 13080 2#30	0:55 1:75	A:17218303;C:11126002;G:12646313;T:32611903;N:28439	55	75	17218303	11126002	12646313	32611903	28439	ERX1036150	ERS790121	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.34009	0.84864	0.33947	0.51553	0.99977	0.99732	0.46268	0.42119	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22326	22326	ERR959102	ERX1036149	ERS790120	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482716	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482716\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 29 sc 1963302\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 29 sc 1963302\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#29	10362822	Illumina sequencing of library 10362822 constructed from sample accession ERS790120 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCCTCAAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#29.cram	cram	144790360.0	1113772.0	SC RUN 13080 2#29	0:55 1:75	A:33936587;C:27790518;G:27553536;T:55458350;N:51369	55	75	33936587	27790518	27553536	55458350	51369	ERX1036149	ERS790120	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.31904	0.63823	0.31749	0.4025	0.99975	0.99594	0.72222	0.23266	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22327	22327	ERR959101	ERX1036148	ERS790119	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482715	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482715\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 28 sc 1963301\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 28 sc 1963301\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#28	10362821	Illumina sequencing of library 10362821 constructed from sample accession ERS790119 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TACAGGAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#28.cram	cram	216795280.0	1667656.0	SC RUN 13080 2#28	0:55 1:75	A:51837367;C:43134622;G:38839352;T:82903687;N:80252	55	75	51837367	43134622	38839352	82903687	80252	ERX1036148	ERS790119	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.40948	0.67835	0.40334	0.55663	0.99979	0.99713	0.38477	0.74764	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22328	22328	ERR959100	ERX1036147	ERS790118	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482714	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:25:39Z\|External Id:SAMEA3482714\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:25:39Z\|INSDC status:public\|Submitter Id:shield cell 27 sc 1963300\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 27 sc 1963300\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#27	10362820	Illumina sequencing of library 10362820 constructed from sample accession ERS790118 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAGTGACT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#27.cram	cram	220939550.0	1699535.0	SC RUN 13080 2#27	0:55 1:75	A:53560329;C:37737879;G:38774386;T:90787623;N:79333	55	75	53560329	37737879	38774386	90787623	79333	ERX1036147	ERS790118	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.35502	0.89331	0.35421	0.307	0.99983	0.99602	0.34177	0.6555	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22329	22329	ERR959099	ERX1036146	ERS790117	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482713	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482713\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 26 sc 1963299\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 26 sc 1963299\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#26	10362819	Illumina sequencing of library 10362819 constructed from sample accession ERS790117 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTCCTGCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#26.cram	cram	141033620.0	1084874.0	SC RUN 13080 2#26	0:55 1:75	A:35600085;C:23528391;G:21846525;T:60007320;N:51299	55	75	35600085	23528391	21846525	60007320	51299	ERX1036146	ERS790117	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.46191	0.72227	0.4582	0.32568	0.99977	0.99569	0.04136	0.32439	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22330	22330	ERR959098	ERX1036145	ERS790116	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482712	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:42:02Z\|External Id:SAMEA3482712\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:42:02Z\|INSDC status:public\|Submitter Id:shield cell 25 sc 1963298\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 25 sc 1963298\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#25	10362818	Illumina sequencing of library 10362818 constructed from sample accession ERS790116 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGCGATCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#25.cram	cram	71199180.0	547686.0	SC RUN 13080 2#25	0:55 1:75	A:18755753;C:11061732;G:11610259;T:29746973;N:24463	55	75	18755753	11061732	11610259	29746973	24463	ERX1036145	ERS790116	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.3774	0.6198	0.37599	0.29621	0.99975	0.99644	0.31325	0.3498	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22331	22331	ERR959097	ERX1036144	ERS790115	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482711	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:25:39Z\|External Id:SAMEA3482711\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:25:39Z\|INSDC status:public\|Submitter Id:shield cell 24 sc 1963297\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTGACTCT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 24 sc 1963297\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#24	10362817	Illumina sequencing of library 10362817 constructed from sample accession ERS790115 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTGACTCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#24.cram	cram	531421410.0	4087857.0	SC RUN 13080 2#24	0:55 1:75	A:139795472;C:85918823;G:95175976;T:210332994;N:198145	55	75	139795472	85918823	95175976	210332994	198145	ERX1036144	ERS790115	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.28457	0.68417	0.27568	0.18923	0.99959	0.99577	0.20502	0.51265	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22332	22332	ERR959096	ERX1036143	ERS790114	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482710	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482710\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 23 sc 1963296\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGCATAGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 23 sc 1963296\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#23	10362816	Illumina sequencing of library 10362816 constructed from sample accession ERS790114 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGCATAGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#23.cram	cram	77469340.0	595918.0	SC RUN 13080 2#23										ERX1036143	ERS790114	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.18149	0.60725	0.18109	0.29736	0.99977	0.99318	0.62686	0.44383	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22333	22333	ERR959095	ERX1036142	ERS790113	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482709	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482709\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 22 sc 1963295\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGATACGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 22 sc 1963295\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#22	10362815	Illumina sequencing of library 10362815 constructed from sample accession ERS790113 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGATACGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#22.cram	cram	548047110.0	4215747.0	SC RUN 13080 2#22	0:55 1:75	A:131358359;C:88356487;G:94996089;T:233143350;N:192825	55	75	131358359	88356487	94996089	233143350	192825	ERX1036142	ERS790113	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.30462	0.88522	0.29477	0.25363	0.99953	0.9947	0.61651	0.49737	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22334	22334	ERR959094	ERX1036141	ERS790112	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482708	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:25:39Z\|External Id:SAMEA3482708\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:25:39Z\|INSDC status:public\|Submitter Id:shield cell 21 sc 1963294\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCGAGCGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 21 sc 1963294\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#21	10362814	Illumina sequencing of library 10362814 constructed from sample accession ERS790112 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCGAGCGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#21.cram	cram	7020.0	54.0	SC RUN 13080 2#21	0:55 1:75	A:2121;C:1388;G:1248;T:2262;N:1	55	75	2121	1388	1248	2262	1	ERX1036141	ERS790112	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.0	0.01852	0.0	0.0	1.0	0.99997		0.0	55	75	T	T	mates < 9% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22335	22335	ERR959093	ERX1036140	ERS790111	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482707	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482707\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 20 sc 1963293\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTGGAGGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 20 sc 1963293\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#20	10362813	Illumina sequencing of library 10362813 constructed from sample accession ERS790111 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTGGAGGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#20.cram	cram	24858470.0	191219.0	SC RUN 13080 2#20	0:55 1:75	A:7016139;C:3920154;G:4027161;T:9885285;N:9731	55	75	7016139	3920154	4027161	9885285	9731	ERX1036140	ERS790111	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.24653	0.75701	0.24619	0.75426	0.99989	0.99616	0.05714	0.36416	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22336	22336	ERR959143	ERX1036190	ERS790161	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482757	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T01:59:33Z\|External Id:SAMEA3482757\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T01:59:33Z\|INSDC status:public\|Submitter Id:shield cell 70 sc 1963343\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GATCTCTT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 70 sc 1963343\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#70	10362863	Illumina sequencing of library 10362863 constructed from sample accession ERS790161 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GATCTCTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#70.cram	cram	42076320.0	323664.0	SC RUN 13080 2#70	0:55 1:75	A:10283791;C:8060365;G:8628297;T:15088767;N:15100	55	75	10283791	8060365	8628297	15088767	15100	ERX1036190	ERS790161	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.4441	0.58989	0.40345	0.03532	0.99981	0.99774	0.9406	0.5011	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22337	22337	ERR959142	ERX1036189	ERS790160	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482756	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:28:39Z\|External Id:SAMEA3482756\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:28:39Z\|INSDC status:public\|Submitter Id:shield cell 69 sc 1963342\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence GGTGAGTT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 69 sc 1963342\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#69	10362862	Illumina sequencing of library 10362862 constructed from sample accession ERS790160 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence GGTGAGTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#69.cram	cram	57359120.0	441224.0	SC RUN 13080 2#69	0:55 1:75	A:15064031;C:11468386;G:11042461;T:19763412;N:20830	55	75	15064031	11468386	11042461	19763412	20830	ERX1036189	ERS790160	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.47318	0.89154	0.472	0.76452	0.99987	0.99795	0.4125	0.76406	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22338	22338	ERR959141	ERX1036188	ERS790159	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482755	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T01:59:33Z\|External Id:SAMEA3482755\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T01:59:33Z\|INSDC status:public\|Submitter Id:shield cell 68 sc 1963341\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGCGTGAA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 68 sc 1963341\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#68	10362861	Illumina sequencing of library 10362861 constructed from sample accession ERS790159 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGCGTGAA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#68.cram	cram	113598680.0	873836.0	SC RUN 13080 2#68	0:55 1:75	A:29660709;C:19656486;G:21234037;T:43004665;N:42783	55	75	29660709	19656486	21234037	43004665	42783	ERX1036188	ERS790159	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.25184	0.69386	0.22988	0.31973	0.99975	0.99661	0.99021	0.16862	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22339	22339	ERR959140	ERX1036187	ERS790158	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482754	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:42:57Z\|External Id:SAMEA3482754\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:42:57Z\|INSDC status:public\|Submitter Id:shield cell 67 sc 1963340\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TACCACCA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 67 sc 1963340\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#67	10362860	Illumina sequencing of library 10362860 constructed from sample accession ERS790158 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TACCACCA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#67.cram	cram	47373430.0	364411.0	SC RUN 13080 2#67	0:55 1:75	A:11989895;C:8641143;G:9669166;T:17054740;N:18486	55	75	11989895	8641143	9669166	17054740	18486	ERX1036187	ERS790158	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.43772	0.73045	0.39011	0.48937	0.99989	0.99864	0.99818	0.49527	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22340	22340	ERR959139	ERX1036186	ERS790157	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482753	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:27:21Z\|External Id:SAMEA3482753\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:27:21Z\|INSDC status:public\|Submitter Id:shield cell 66 sc 1963339\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGAAGCCA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 66 sc 1963339\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#66	10362859	Illumina sequencing of library 10362859 constructed from sample accession ERS790157 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGAAGCCA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#66.cram	cram	146879980.0	1129846.0	SC RUN 13080 2#66	0:55 1:75	A:37829300;C:29024709;G:28251706;T:51721679;N:52586	55	75	37829300	29024709	28251706	51721679	52586	ERX1036186	ERS790157	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.33722	0.47961	0.3369	0.39074	0.99991	0.99831	0.04166	0.20674	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22341	22341	ERR959138	ERX1036185	ERS790156	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482752	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T01:59:33Z\|External Id:SAMEA3482752\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T01:59:33Z\|INSDC status:public\|Submitter Id:shield cell 65 sc 1963338\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTGTTCCA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 65 sc 1963338\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#65	10362858	Illumina sequencing of library 10362858 constructed from sample accession ERS790156 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTGTTCCA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#65.cram	cram	132408250.0	1018525.0	SC RUN 13080 2#65	0:55 1:75	A:30597456;C:26266730;G:24874939;T:50618622;N:50503	55	75	30597456	26266730	24874939	50618622	50503	ERX1036185	ERS790156	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.28218	0.64124	0.27596	0.3867	0.99987	0.99715	0.94096	0.22648	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22342	22342	ERR959137	ERX1036184	ERS790155	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482751	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:39Z\|ENA LAST UPDATE:2018 03 09T02:15:42Z\|External Id:SAMEA3482751\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:39Z\|INSDC last update:2018 03 09T02:15:42Z\|INSDC status:public\|Submitter Id:shield cell 64 sc 1963337\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCTCTTCA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 64 sc 1963337\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#64	10362857	Illumina sequencing of library 10362857 constructed from sample accession ERS790155 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCTCTTCA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#64.cram	cram	290418440.0	2233988.0	SC RUN 13080 2#64	0:55 1:75	A:67788061;C:43676665;G:52635825;T:126215707;N:102182	55	75	67788061	43676665	52635825	126215707	102182	ERX1036184	ERS790155	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.35337	0.7003	0.35175	0.214	0.99975	0.99429	0.37931	0.49134	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22343	22343	ERR959136	ERX1036183	ERS790154	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482750	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:27:21Z\|External Id:SAMEA3482750\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:27:21Z\|INSDC status:public\|Submitter Id:shield cell 63 sc 1963336\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGTGAAGA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 63 sc 1963336\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#63	10362856	Illumina sequencing of library 10362856 constructed from sample accession ERS790154 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGTGAAGA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#63.cram	cram	419926000.0	3230200.0	SC RUN 13080 2#63	0:55 1:75	A:101336663;C:69419526;G:74710153;T:174308501;N:151157	55	75	101336663	69419526	74710153	174308501	151157	ERX1036183	ERS790154	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.31431	0.85933	0.30986	0.26757	0.99963	0.99624	0.39687	0.42044	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22344	22344	ERR959135	ERX1036182	ERS790153	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482749	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482749\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 62 sc 1963335\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAGACGGA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 62 sc 1963335\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#62	10362855	Illumina sequencing of library 10362855 constructed from sample accession ERS790153 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAGACGGA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#62.cram	cram	94867760.0	729752.0	SC RUN 13080 2#62	0:55 1:75	A:24304886;C:18771228;G:19322341;T:32433772;N:35533	55	75	24304886	18771228	19322341	32433772	35533	ERX1036182	ERS790153	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.68249	0.75225	0.68178	0.68248	0.99989	0.99746	0.05769	0.98399	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22345	22345	ERR959134	ERX1036181	ERS790152	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482748	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:42:56Z\|External Id:SAMEA3482748\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:42:56Z\|INSDC status:public\|Submitter Id:shield cell 61 sc 1963334\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGCTGATA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 61 sc 1963334\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#61	10362854	Illumina sequencing of library 10362854 constructed from sample accession ERS790152 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGCTGATA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#61.cram	cram	127163790.0	978183.0	SC RUN 13080 2#61	0:55 1:75	A:31739847;C:26014935;G:24168739;T:45194957;N:45312	55	75	31739847	26014935	24168739	45194957	45312	ERX1036181	ERS790152	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.50735	0.51895	0.50594	0.50598	0.99985	0.99681	0.48148	0.76836	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22346	22346	ERR959133	ERX1036180	ERS790151	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482747	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:27:21Z\|External Id:SAMEA3482747\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:27:21Z\|INSDC status:public\|Submitter Id:shield cell 60 sc 1963333\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCATCCTA is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 60 sc 1963333\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#60	10362853	Illumina sequencing of library 10362853 constructed from sample accession ERS790151 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCATCCTA.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#60.cram	cram	22215960.0	170892.0	SC RUN 13080 2#60	0:55 1:75	A:5126582;C:4205343;G:2581949;T:10294674;N:7412	55	75	5126582	4205343	2581949	10294674	7412	ERX1036180	ERS790151	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.65238	0.44035	0.65138	0.05103	0.99989	0.99636	0.06593	0.99557	55	75	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22347	22347	ERR959132	ERX1036179	ERS790150	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482746	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482746\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 59 sc 1963332\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAGAACAC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 59 sc 1963332\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#59	10362852	Illumina sequencing of library 10362852 constructed from sample accession ERS790150 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAGAACAC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#59.cram	cram	60397610.0	464597.0	SC RUN 13080 2#59	0:55 1:75	A:16318469;C:11873938;G:11947113;T:20235218;N:22872	55	75	16318469	11873938	11947113	20235218	22872	ERX1036179	ERS790150	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.23907	0.60205	0.23893	0.30623	0.99991	0.99853	0.11111	0.00066	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22348	22348	ERR959131	ERX1036178	ERS790149	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482745	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482745\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 58 sc 1963331\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGACAGAC is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 58 sc 1963331\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#58	10362851	Illumina sequencing of library 10362851 constructed from sample accession ERS790149 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGACAGAC.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#58.cram	cram	35237540.0	271058.0	SC RUN 13080 2#58	0:55 1:75	A:8129333;C:8221277;G:6782760;T:12091129;N:13041	55	75	8129333	8221277	6782760	12091129	13041	ERX1036178	ERS790149	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.43685	0.78734	0.43681	0.78719	0.99995	0.99953	0.0	0.48	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22349	22349	ERR959117	ERX1036164	ERS790135	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482731	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482731\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 44 sc 1963317\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGGCTCAG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 44 sc 1963317\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#44	10362837	Illumina sequencing of library 10362837 constructed from sample accession ERS790135 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGGCTCAG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#44.cram	cram	40370590.0	310543.0	SC RUN 13080 2#44	0:55 1:75	A:9236436;C:8751556;G:8170538;T:14197162;N:14898	55	75	9236436	8751556	8170538	14197162	14898	ERX1036164	ERS790135	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.34033	0.44678	0.34032	0.44666	1.0	0.99965		0.42105	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22350	22350	ERR959116	ERX1036163	ERS790134	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482730	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:42:02Z\|External Id:SAMEA3482730\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:42:02Z\|INSDC status:public\|Submitter Id:shield cell 43 sc 1963316\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 43 sc 1963316\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#43	10362836	Illumina sequencing of library 10362836 constructed from sample accession ERS790134 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCATTGAG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#43.cram	cram	36952110.0	284247.0	SC RUN 13080 2#43	0:55 1:75	A:9146273;C:7957658;G:7545604;T:12289123;N:13452	55	75	9146273	7957658	7545604	12289123	13452	ERX1036163	ERS790134	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.04135	0.90769	0.03812	0.5207	0.99993	0.99859	0.33108	0.39899	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22351	22351	ERR959115	ERX1036162	ERS790133	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482729	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482729\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 42 sc 1963315\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGTATGCG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 42 sc 1963315\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#42	10362835	Illumina sequencing of library 10362835 constructed from sample accession ERS790133 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGTATGCG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#42.cram	cram	37820900.0	290930.0	SC RUN 13080 2#42	0:55 1:75	A:8629157;C:8139187;G:8013925;T:13024294;N:14337	55	75	8629157	8139187	8013925	13024294	14337	ERX1036162	ERS790133	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.58238	0.33696	0.58167	0.32883	0.99993	0.99969	0.95454	0.95418	55	75	B	T	mate2 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22352	22352	ERR959114	ERX1036161	ERS790132	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482728	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:15:41Z\|External Id:SAMEA3482728\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:15:41Z\|INSDC status:public\|Submitter Id:shield cell 41 sc 1963314\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCCAGTCG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 41 sc 1963314\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#41	10362834	Illumina sequencing of library 10362834 constructed from sample accession ERS790132 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCCAGTCG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#41.cram	cram	25582960.0	196792.0	SC RUN 13080 2#41	0:55 1:75	A:5244786;C:6119041;G:5025898;T:9184142;N:9093	55	75	5244786	6119041	5025898	9184142	9093	ERX1036161	ERS790132	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.72926	0.56706	0.72888	0.5663	0.99991	0.99849	0.0625	0.59036	55	75	B	T	nofeature rate indicates technical or non-transcriptomic	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22353	22353	ERR959113	ERX1036160	ERS790131	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482727	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482727\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 40 sc 1963313\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAAGTTCG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 40 sc 1963313\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#40	10362833	Illumina sequencing of library 10362833 constructed from sample accession ERS790131 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAAGTTCG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#40.cram	cram	108501770.0	834629.0	SC RUN 13080 2#40	0:55 1:75	A:27094140;C:24187718;G:20757050;T:36421483;N:41379	55	75	27094140	24187718	20757050	36421483	41379	ERX1036160	ERS790131	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.59407	0.83571	0.59349	0.7686	0.99987	0.99835	0.35714	0.00336	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22354	22354	ERR959112	ERX1036159	ERS790130	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482726	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482726\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 39 sc 1963312\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 39 sc 1963312\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#39	10362832	Illumina sequencing of library 10362832 constructed from sample accession ERS790130 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCAGGAGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#39.cram	cram	24700000.0	190000.0	SC RUN 13080 2#39	0:55 1:75	A:6019216;C:5458025;G:5093824;T:8119874;N:9061	55	75	6019216	5458025	5093824	8119874	9061	ERX1036159	ERS790130	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.48938	0.62623	0.48904	0.40978	0.99991	0.99817	0.6923	0.00138	55	75	B	B	biological fallback assumption	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22355	22355	ERR959111	ERX1036158	ERS790129	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482725	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482725\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 38 sc 1963311\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 38 sc 1963311\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#38	10362831	Illumina sequencing of library 10362831 constructed from sample accession ERS790129 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCTCACGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#38.cram	cram	46402200.0	356940.0	SC RUN 13080 2#38	0:55 1:75	A:10196520;C:10030552;G:8857083;T:17301627;N:16418	55	75	10196520	10030552	8857083	17301627	16418	ERX1036158	ERS790129	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.28086	0.81547	0.26667	0.44955	0.99995	0.99825	0.99483	0.97284	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22356	22356	ERR959110	ERX1036157	ERS790128	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482724	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:42:02Z\|External Id:SAMEA3482724\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:42:02Z\|INSDC status:public\|Submitter Id:shield cell 37 sc 1963310\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 37 sc 1963310\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#37	10362830	Illumina sequencing of library 10362830 constructed from sample accession ERS790128 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TACTTCGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#37.cram	cram	102368110.0	787447.0	SC RUN 13080 2#37	0:55 1:75	A:26901671;C:18056097;G:15646052;T:41726812;N:37478	55	75	26901671	18056097	15646052	41726812	37478	ERX1036157	ERS790128	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.31136	0.61466	0.31039	0.36513	0.99985	0.99549	0.39622	0.85117	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22357	22357	ERR959109	ERX1036156	ERS790127	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482723	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482723\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 36 sc 1963309\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 36 sc 1963309\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#36	10362829	Illumina sequencing of library 10362829 constructed from sample accession ERS790127 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TGAACTGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#36.cram	cram	113186450.0	870665.0	SC RUN 13080 2#36	0:55 1:75	A:28195279;C:18750171;G:19790754;T:46410133;N:40113	55	75	28195279	18750171	19790754	46410133	40113	ERX1036156	ERS790127	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.28754	0.59901	0.28646	0.10508	0.99985	0.99551	0.42857	0.59809	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22358	22358	ERR959108	ERX1036155	ERS790126	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482722	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482722\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 35 sc 1963308\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 35 sc 1963308\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#35	10362828	Illumina sequencing of library 10362828 constructed from sample accession ERS790126 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TTGGTATG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#35.cram	cram	88292230.0	679171.0	SC RUN 13080 2#35	0:55 1:75	A:23035745;C:16155411;G:16840156;T:32228577;N:32341	55	75	23035745	16155411	16840156	32228577	32341	ERX1036155	ERS790126	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.24696	0.43107	0.24669	0.18751	0.99989	0.99732	0.28571	0.1954	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22359	22359	ERR959107	ERX1036154	ERS790125	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482721	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:14:54Z\|External Id:SAMEA3482721\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:14:54Z\|INSDC status:public\|Submitter Id:shield cell 34 sc 1963307\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 34 sc 1963307\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#34	10362827	Illumina sequencing of library 10362827 constructed from sample accession ERS790125 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TAACGCTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#34.cram	cram	50728080.0	390216.0	SC RUN 13080 2#34	0:55 1:75	A:11558127;C:10003161;G:8823963;T:20324139;N:18690	55	75	11558127	10003161	8823963	20324139	18690	ERX1036154	ERS790125	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.36584	0.49038	0.36498	0.4289	0.99985	0.99588	0.15662	0.01963	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22360	22360	ERR959106	ERX1036153	ERS790124	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482720	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:39Z\|ENA LAST UPDATE:2018 03 09T02:27:20Z\|External Id:SAMEA3482720\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:39Z\|INSDC last update:2018 03 09T02:27:20Z\|INSDC status:public\|Submitter Id:shield cell 33 sc 1963306\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 33 sc 1963306\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#33	10362826	Illumina sequencing of library 10362826 constructed from sample accession ERS790124 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCGAAGTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#33.cram	cram	21945430.0	168811.0	SC RUN 13080 2#33	0:55 1:75	A:4930918;C:5059230;G:4886784;T:7060484;N:8014	55	75	4930918	5059230	4886784	7060484	8014	ERX1036153	ERS790124	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.0	9e-05	0.0	1e-05	1.0	0.99985		0.57142	55	75	T	T	mates < 9% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22361	22361	ERR959092	ERX1036139	ERS790110	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482706	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:42:02Z\|External Id:SAMEA3482706\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:42:02Z\|INSDC status:public\|Submitter Id:shield cell 19 sc 1963292\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single shield cells. A 8 base indexing sequence TCTGCTGT is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:shield cell 19 sc 1963292\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 13080 2#19	10362812	Illumina sequencing of library 10362812 constructed from sample accession ERS790110 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 13080 2. This submission includes reads tagged with the sequence TCTGCTGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	13080_2#19.cram	cram	239438420.0	1841834.0	SC RUN 13080 2#19	0:55 1:75	A:59697696;C:44290471;G:44084190;T:91278474;N:87589	55	75	59697696	44290471	44084190	91278474	87589	ERX1036139	ERS790110	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.31829	0.81349	0.2851	0.3492	0.99977	0.99699	0.19346	0.46707	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22362	22362	ERR958788	ERX1035835	ERS790016	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482612	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:40Z\|ENA LAST UPDATE:2018 03 09T02:20:51Z\|External Id:SAMEA3482612\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:40Z\|INSDC last update:2018 03 09T02:20:51Z\|INSDC status:public\|Submitter Id:Shield cell B3 sc 1884424\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:Shield cell B3 sc 1884424\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#39	9702684	Illumina sequencing of library 9702684 constructed from sample accession ERS790016 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TCAGGAGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#39.cram	cram	212977700.0	1638290.0	SC RUN 12487 1#39	0:55 1:75	A:52959206;C:41280548;G:38924505;T:79787196;N:26245	55	75	52959206	41280548	38924505	79787196	26245	ERX1035835	ERS790016	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.45258	0.80674	0.43564	0.58959	0.99906	0.99752	0.62443	0.55477	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22363	22363	ERR958787	ERX1035834	ERS790015	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482611	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:11:13Z\|External Id:SAMEA3482611\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:11:13Z\|INSDC status:public\|Submitter Id:Shield cell B2 sc 1884423\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:Shield cell B2 sc 1884423\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#38	9702683	Illumina sequencing of library 9702683 constructed from sample accession ERS790015 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TCTCACGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#38.cram	cram	308481940.0	2372938.0	SC RUN 12487 1#38	0:55 1:75	A:76962566;C:56530866;G:56846952;T:118104217;N:37339	55	75	76962566	56530866	56846952	118104217	37339	ERX1035834	ERS790015	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.53388	0.853	0.52885	0.63347	0.99963	0.99707	0.4614	0.52765	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22364	22364	ERR958786	ERX1035833	ERS790014	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482610	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:56:13Z\|External Id:SAMEA3482610\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:56:13Z\|INSDC status:public\|Submitter Id:Shield cell B1 sc 1884422\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:Shield cell B1 sc 1884422\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#37	9702682	Illumina sequencing of library 9702682 constructed from sample accession ERS790014 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TACTTCGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#37.cram	cram	1102146370.0	8478049.0	SC RUN 12487 1#37	0:55 1:75	A:274032451;C:174713693;G:190977037;T:462284024;N:139165	55	75	274032451	174713693	190977037	462284024	139165	ERX1035833	ERS790014	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.3477	0.84909	0.33388	0.30911	0.99855	0.98999	0.51063	0.57485	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22365	22365	ERR958785	ERX1035832	ERS790013	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482609	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:42Z\|ENA LAST UPDATE:2018 03 09T02:20:51Z\|External Id:SAMEA3482609\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:42Z\|INSDC last update:2018 03 09T02:20:51Z\|INSDC status:public\|Submitter Id:animal pole cell A15 sc 1884421\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A15 sc 1884421\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#36	9702681	Illumina sequencing of library 9702681 constructed from sample accession ERS790013 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TGAACTGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#36.cram	cram	307922680.0	2368636.0	SC RUN 12487 1#36	0:55 1:75	A:74934219;C:63528400;G:56950290;T:112470018;N:39753	55	75	74934219	63528400	56950290	112470018	39753	ERX1035832	ERS790013	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.52087	0.80034	0.51853	0.70199	0.99971	0.99837	0.58461	0.47072	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22366	22366	ERR958784	ERX1035831	ERS790012	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482608	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:09:52Z\|External Id:SAMEA3482608\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:09:52Z\|INSDC status:public\|Submitter Id:animal pole cell A14 sc 1884420\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A14 sc 1884420\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#35	9702680	Illumina sequencing of library 9702680 constructed from sample accession ERS790012 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TTGGTATG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#35.cram	cram	275255890.0	2117353.0	SC RUN 12487 1#35	0:55 1:75	A:69255185;C:55339798;G:52907345;T:97720876;N:32686	55	75	69255185	55339798	52907345	97720876	32686	ERX1035831	ERS790012	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.52241	0.72446	0.52184	0.63219	0.99981	0.99931	0.60937	0.31582	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22367	22367	ERR958783	ERX1035830	ERS790011	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482607	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:09:51Z\|External Id:SAMEA3482607\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:09:51Z\|INSDC status:public\|Submitter Id:animal pole cell A13 sc 1884419\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A13 sc 1884419\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#34	9702679	Illumina sequencing of library 9702679 constructed from sample accession ERS790011 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TAACGCTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#34.cram	cram	315658200.0	2428140.0	SC RUN 12487 1#34	0:55 1:75	A:77133242;C:60743970;G:57511024;T:120231319;N:38645	55	75	77133242	60743970	57511024	120231319	38645	ERX1035830	ERS790011	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.47354	0.78005	0.46318	0.59792	0.99943	0.99786	0.50603	0.64168	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22368	22368	ERR958782	ERX1035829	ERS790010	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482606	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:41Z\|ENA LAST UPDATE:2018 03 09T02:20:51Z\|External Id:SAMEA3482606\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:41Z\|INSDC last update:2018 03 09T02:20:51Z\|INSDC status:public\|Submitter Id:animal pole cell A12 sc 1884418\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A12 sc 1884418\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#33	9702678	Illumina sequencing of library 9702678 constructed from sample accession ERS790010 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TCGAAGTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#33.cram	cram	65774410.0	505957.0	SC RUN 12487 1#33	0:55 1:75	A:15955976;C:12266598;G:11288201;T:26255799;N:7836	55	75	15955976	12266598	11288201	26255799	7836	ERX1035829	ERS790010	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.4044	0.8229	0.40247	0.6854	0.99981	0.99967	0.97356	0.51398	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22369	22369	ERR958781	ERX1035828	ERS790009	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482605	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:44Z\|ENA LAST UPDATE:2018 03 09T02:09:51Z\|External Id:SAMEA3482605\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:44Z\|INSDC last update:2018 03 09T02:09:51Z\|INSDC status:public\|Submitter Id:animal pole cell A11 sc 1884417\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A11 sc 1884417\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#32	9702677	Illumina sequencing of library 9702677 constructed from sample accession ERS790009 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TTCCATTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#32.cram	cram	392158130.0	3016601.0	SC RUN 12487 1#32	0:55 1:75	A:97326607;C:76618852;G:71845551;T:146317946;N:49174	55	75	97326607	76618852	71845551	146317946	49174	ERX1035828	ERS790009	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.46707	0.82954	0.46239	0.67737	0.99928	0.99748	0.88321	0.50914	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22370	22370	ERR958780	ERX1035827	ERS790008	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482604	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:43Z\|ENA LAST UPDATE:2018 03 09T02:56:13Z\|External Id:SAMEA3482604\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:43Z\|INSDC last update:2018 03 09T02:56:13Z\|INSDC status:public\|Submitter Id:animal pole cell A10 sc 1884416\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A10 sc 1884416\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#31	9702676	Illumina sequencing of library 9702676 constructed from sample accession ERS790008 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TAGTCTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#31.cram	cram	245171030.0	1885931.0	SC RUN 12487 1#31	0:55 1:75	A:63296073;C:47422785;G:45427281;T:88994334;N:30557	55	75	63296073	47422785	45427281	88994334	30557	ERX1035827	ERS790008	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.43707	0.74994	0.43211	0.58314	0.99949	0.99719	0.99369	0.65584	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise
22371	22371	ERR958779	ERX1035826	ERS790007	ERP011007	PRJEB9859	Transcriptome profiling of single zebrafish cells	Transcriptome_profiling_of_single_zebrafish_cells-sc-2991	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from individual wild type zebrafish cells. Generated to study the transcriptome of single cells.			SAMEA3482603	SC	ArrayExpress DevelopmentalStage:6 hpf\|ArrayExpress Genotype:T/LF\|ArrayExpress Phenotype:WT\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2015 07 13T15:15:45Z\|ENA LAST UPDATE:2018 03 09T02:20:51Z\|External Id:SAMEA3482603\|INSDC center name:SC\|INSDC first public:2015 07 13T15:15:45Z\|INSDC last update:2018 03 09T02:20:51Z\|INSDC status:public\|Submitter Id:animal pole cell A9 sc 1884415\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single cells. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by GC and polyT.\|sample name:animal pole cell A9 sc 1884415\|scientific name:Danio rerio\|strain:T/LF	Illumina HiSeq 2500 paired end sequencing	SC EXP 12487 1#30	9702675	Illumina sequencing of library 9702675 constructed from sample accession ERS790007 for study accession ERP011007. This is part of an Illumina multiplexed sequencing run 12487 1. This submission includes reads tagged with the sequence TGTGGTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP011007	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2015 07 16\|ENA LAST UPDATE:2018 11 16	12487_1#30.cram	cram	250389750.0	1926075.0	SC RUN 12487 1#30	0:55 1:75	A:63230724;C:48198346;G:46265869;T:92666012;N:28799	55	75	63230724	48198346	46265869	92666012	28799	ERX1035826	ERS790007	ERA457908	The Wellcome Trust Sanger Institute\|European Nucleotide Archive	Wellcome Sanger Institute	2	0.51357	0.78383	0.51016	0.59901	0.99973	0.9987	0.08048	0.63331	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2015-07-13	Gastrula	Embryo	Undetermined	Embryo Imprecise

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;