RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

144 rows where devstage_curation = "Pharyngula" and technology = "celseq"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation 5

experiment.library_layout 2

technology 1

  • celseq · 144 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 144 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor 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.r3_length run.r4_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 tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
38364 38364 SRR1793802 SRX869237 SRS840014 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0012 GSM1604058   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0012 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604058 GSM1604058: d red ZF sample 0012; Danio rerio; RNA Seq GSM1604058   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0012.fastq.gz fastq 136949295.0 3912837.0 GSM1604058 r1 0:35 A:38967686;C:29235653;G:29781723;T:38764742;N:199491 35       38967686 29235653 29781723 38764742 199491 SRX869237 SRS840014 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.50546   0.22201   0.91524   0.49457   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38365 38365 SRR1793801 SRX869236 SRS840015 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0008 GSM1604057   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0008 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604057 GSM1604057: d red ZF sample 0008; Danio rerio; RNA Seq GSM1604057   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0008.fastq.gz fastq 230204380.0 6577268.0 GSM1604057 r1 0:35 A:63286154;C:49924891;G:50948035;T:65703538;N:341762 35       63286154 49924891 50948035 65703538 341762 SRX869236 SRS840015 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.59898   0.14092   0.89073   0.49292   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38366 38366 SRR1793800 SRX869235 SRS840013 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0011 GSM1604056   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0011 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604056 GSM1604056: V red ZF sample 0011; Danio rerio; RNA Seq GSM1604056   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0011.fastq.gz fastq 146319705.0 4180563.0 GSM1604056 r1 0:35 A:40991954;C:30892087;G:32112709;T:42103782;N:219173 35       40991954 30892087 32112709 42103782 219173 SRX869235 SRS840013 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57038   0.16086   0.89014   0.53016   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38367 38367 SRR1793799 SRX869234 SRS840016 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0007 GSM1604055   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0007 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604055 GSM1604055: V red ZF sample 0007; Danio rerio; RNA Seq GSM1604055   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0007.fastq.gz fastq 219537045.0 6272487.0 GSM1604055 r1 0:35 A:61562432;C:46586451;G:48274564;T:62792331;N:321267 35       61562432 46586451 48274564 62792331 321267 SRX869234 SRS840016 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57949   0.1659   0.88187   0.51446   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
40631 40631 SRR3231322 SRX1637097 SRS1342906 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   8and24hpf wt Plate1.1 GSM2090863   tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 8and24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090863 GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090863   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090863 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     8and24hpf_wt_Plate1.1_R1_001.fastq.gz 8and24hpf_wt_Plate1.1_R2_001.fastq.gz fastq fastq 354951269.0 2354572.0 GSM2090863 r1 0:75.37 1:75.38 A:109255676;C:46649925;G:56800706;T:142212324;N:32638 75 75     109255676 46649925 56800706 142212324 32638 SRX1637097 SRS1342906 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.08814 0.58586 0.05414 0.12777 0.98236 0.8253 0.52224 0.5333 75 55 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40632 40632 SRR3231323 SRX1637097 SRS1342906 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   8and24hpf wt Plate1.1 GSM2090863   tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 8and24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090863 GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090863   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090863 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     8and24hpf_wt_Plate1.2_R1_001.fastq.gz 8and24hpf_wt_Plate1.2_R2_001.fastq.gz fastq fastq 373175186.0 2475371.0 GSM2090863 r2 0:75.37 1:75.38 A:114080796;C:49251081;G:59964869;T:149836843;N:41597 75 75     114080796 49251081 59964869 149836843 41597 SRX1637097 SRS1342906 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.0895 0.59282 0.05309 0.12622 0.9811 0.82185 0.51449 0.52518 75 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40633 40633 SRR3231324 SRX1637097 SRS1342906 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   8and24hpf wt Plate1.1 GSM2090863   tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 8and24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090863 GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090863   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090863 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     8and24hpf_wt_Plate1.3_R1_001.fastq.gz 8and24hpf_wt_Plate1.3_R2_001.fastq.gz fastq fastq 376796544.0 2499144.0 GSM2090863 r3 0:75.38 1:75.39 A:114262594;C:49685044;G:61341084;T:151464220;N:43602 75 75     114262594 49685044 61341084 151464220 43602 SRX1637097 SRS1342906 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.08885 0.60874 0.05444 0.12569 0.98177 0.81233 0.51071 0.53112 75 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40634 40634 SRR3231325 SRX1637097 SRS1342906 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   8and24hpf wt Plate1.1 GSM2090863   tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 8and24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090863 GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090863   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090863 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     8and24hpf_wt_Plate1_R1_001.fastq.gz 8and24hpf_wt_Plate1_R2_001.fastq.gz fastq fastq 370852802.0 2459988.0 GSM2090863 r4 0:75.37 1:75.38 A:113706258;C:48924259;G:59523739;T:148663433;N:35113 75 75     113706258 48924259 59523739 148663433 35113 SRX1637097 SRS1342906 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.08962 0.59214 0.05376 0.12667 0.98226 0.82142 0.53851 0.52744 75 32 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40669 40669 SRR3231284 SRX1637085 SRS1342918 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate5.1 GSM2090851   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate5.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090851 GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq GSM2090851   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090851 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate5.1_R1_001.fastq.gz 24hpf_wt_Plate5.1_R2_001.fastq.gz fastq fastq 558605417.0 3704499.0 GSM2090851 r1 0:75.45 1:75.34 A:170059730;C:87004627;G:101477517;T:200008732;N:54811 75 75     170059730 87004627 101477517 200008732 54811 SRX1637085 SRS1342918 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01541 0.18137 0.00841 0.03816 0.99206 0.90047 0.55425 0.56591 76 32 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40670 40670 SRR3231285 SRX1637085 SRS1342918 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate5.1 GSM2090851   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate5.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090851 GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq GSM2090851   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090851 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate5.2_R1_001.fastq.gz 24hpf_wt_Plate5.2_R2_001.fastq.gz fastq fastq 581533785.0 3856402.0 GSM2090851 r2 0:75.45 1:75.34 A:176436951;C:90826765;G:105424561;T:208785606;N:59902 75 75     176436951 90826765 105424561 208785606 59902 SRX1637085 SRS1342918 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01519 0.18239 0.0089 0.03729 0.99306 0.89917 0.59594 0.573 74 75 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40671 40671 SRR3231286 SRX1637085 SRS1342918 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate5.1 GSM2090851   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate5.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090851 GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq GSM2090851   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090851 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate5.3_R1_001.fastq.gz 24hpf_wt_Plate5.3_R2_001.fastq.gz fastq fastq 581069691.0 3853089.0 GSM2090851 r3 0:75.45 1:75.35 A:175088129;C:90460041;G:106640639;T:208812858;N:68024 75 75     175088129 90460041 106640639 208812858 68024 SRX1637085 SRS1342918 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01551 0.19274 0.00932 0.0399 0.99289 0.89319 0.57195 0.56478 74 75 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40672 40672 SRR3231287 SRX1637085 SRS1342918 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate5.1 GSM2090851   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate5.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090851 GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq GSM2090851   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090851 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate5_R1_001.fastq.gz 24hpf_wt_Plate5_R2_001.fastq.gz fastq fastq 576677563.0 3824304.0 GSM2090851 r4 0:75.45 1:75.34 A:175248120;C:90164865;G:104482050;T:206728496;N:54032 75 75     175248120 90164865 104482050 206728496 54032 SRX1637085 SRS1342918 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01561 0.18528 0.00921 0.03947 0.99302 0.8981 0.60185 0.58278 76 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40673 40673 SRR3231280 SRX1637084 SRS1342920 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate4.1 GSM2090850   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate4.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090850 GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq GSM2090850   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090850 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate4.1_R1_001.fastq.gz 24hpf_wt_Plate4.1_R2_001.fastq.gz fastq fastq 739151929.0 4905477.0 GSM2090850 r1 0:75.40 1:75.28 A:237453179;C:120215450;G:139806121;T:241606048;N:71131 75 75     237453179 120215450 139806121 241606048 71131 SRX1637084 SRS1342920 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01446 0.18296 0.00907 0.03633 0.99442 0.91147 0.57858 0.55259 76 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40674 40674 SRR3231281 SRX1637084 SRS1342920 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate4.1 GSM2090850   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate4.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090850 GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq GSM2090850   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090850 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate4.2_R1_001.fastq.gz 24hpf_wt_Plate4.2_R2_001.fastq.gz fastq fastq 769081502.0 5103797.0 GSM2090850 r2 0:75.40 1:75.29 A:245920087;C:125753713;G:145142187;T:252183239;N:82276 75 75     245920087 125753713 145142187 252183239 82276 SRX1637084 SRS1342920 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01429 0.18495 0.00907 0.0378 0.99435 0.91181 0.60136 0.5509 76 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40675 40675 SRR3231282 SRX1637084 SRS1342920 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate4.1 GSM2090850   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate4.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090850 GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq GSM2090850   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090850 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate4.3_R1_001.fastq.gz 24hpf_wt_Plate4.3_R2_001.fastq.gz fastq fastq 763478256.0 5066455.0 GSM2090850 r3 0:75.40 1:75.29 A:242520066;C:123970168;G:146100841;T:250803049;N:84132 75 75     242520066 123970168 146100841 250803049 84132 SRX1637084 SRS1342920 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01481 0.1935 0.0093 0.03777 0.99448 0.90526 0.5546 0.56044 74 75 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40676 40676 SRR3231283 SRX1637084 SRS1342920 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate4.1 GSM2090850   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate4.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090850 GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq GSM2090850   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090850 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate4_R1_001.fastq.gz 24hpf_wt_Plate4_R2_001.fastq.gz fastq fastq 762348830.0 5059335.0 GSM2090850 r4 0:75.40 1:75.28 A:244240563;C:124701855;G:143859660;T:249474441;N:72311 75 75     244240563 124701855 143859660 249474441 72311 SRX1637084 SRS1342920 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01537 0.18668 0.00965 0.03681 0.99407 0.91066 0.54926 0.55097 76 75 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40677 40677 SRR3231276 SRX1637083 SRS1342919 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate3.1 GSM2090849   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090849 GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq GSM2090849   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate3.1_R1_001.fastq.gz 24hpf_wt_Plate3.1_R2_001.fastq.gz fastq fastq 692753746.0 4593127.0 GSM2090849 r1 0:75.47 1:75.35 A:200412235;C:124307113;G:146191995;T:221774807;N:67596 75 75     200412235 124307113 146191995 221774807 67596 SRX1637083 SRS1342919 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.00405 0.02858 0.00276 0.00696 0.99752 0.9722 0.64935 0.55705 76 74 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40678 40678 SRR3231277 SRX1637083 SRS1342919 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate3.1 GSM2090849   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090849 GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq GSM2090849   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate3.2_R1_001.fastq.gz 24hpf_wt_Plate3.2_R2_001.fastq.gz fastq fastq 701569969.0 4651611.0 GSM2090849 r2 0:75.47 1:75.35 A:203675895;C:126097325;G:146891489;T:224837147;N:68113 75 75     203675895 126097325 146891489 224837147 68113 SRX1637083 SRS1342919 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.00395 0.0305 0.0027 0.00699 0.9976 0.97088 0.4863 0.57133 76 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40679 40679 SRR3231278 SRX1637083 SRS1342919 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate3.1 GSM2090849   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090849 GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq GSM2090849   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate3.3_R1_001.fastq.gz 24hpf_wt_Plate3.3_R2_001.fastq.gz fastq fastq 688668111.0 4566244.0 GSM2090849 r3 0:75.47 1:75.35 A:199652330;C:123454100;G:144848134;T:220657099;N:56448 75 75     199652330 123454100 144848134 220657099 56448 SRX1637083 SRS1342919 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.00369 0.02792 0.00272 0.00658 0.99803 0.9727 0.50427 0.55885 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40680 40680 SRR3231279 SRX1637083 SRS1342919 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate3.1 GSM2090849   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090849 GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq GSM2090849   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate3_R1_001.fastq.gz 24hpf_wt_Plate3_R2_001.fastq.gz fastq fastq 702507993.0 4657860.0 GSM2090849 r4 0:75.47 1:75.35 A:203715514;C:126718380;G:147182176;T:224817151;N:74772 75 75     203715514 126718380 147182176 224817151 74772 SRX1637083 SRS1342919 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.00392 0.0275 0.00279 0.00707 0.99778 0.97297 0.46666 0.56022 76 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40681 40681 SRR3231272 SRX1637082 SRS1342921 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate2.1 GSM2090848   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090848 GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq GSM2090848   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090848 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate2.1_R1_001.fastq.gz 24hpf_wt_Plate2.1_R2_001.fastq.gz fastq fastq 298994170.0 1982738.0 GSM2090848 r1 0:75.44 1:75.35 A:93083508;C:44907251;G:52817440;T:108158577;N:27394 75 75     93083508 44907251 52817440 108158577 27394 SRX1637082 SRS1342921 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01409 0.02745 0.01105 0.00689 0.99847 0.97512 0.14754 0.54124 75 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40682 40682 SRR3231273 SRX1637082 SRS1342921 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate2.1 GSM2090848   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090848 GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq GSM2090848   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090848 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate2.2_R1_001.fastq.gz 24hpf_wt_Plate2.2_R2_001.fastq.gz fastq fastq 306815504.0 2034672.0 GSM2090848 r2 0:75.44 1:75.36 A:95967069;C:46066723;G:53601976;T:111150011;N:29725 75 75     95967069 46066723 53601976 111150011 29725 SRX1637082 SRS1342921 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01382 0.03079 0.01075 0.00723 0.99859 0.97344 0.14334 0.56436 75 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40683 40683 SRR3231274 SRX1637082 SRS1342921 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate2.1 GSM2090848   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090848 GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq GSM2090848   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090848 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate2.3_R1_001.fastq.gz 24hpf_wt_Plate2.3_R2_001.fastq.gz fastq fastq 300764521.0 1994537.0 GSM2090848 r3 0:75.44 1:75.35 A:93852241;C:45007343;G:52938896;T:108939437;N:26604 75 75     93852241 45007343 52938896 108939437 26604 SRX1637082 SRS1342921 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.0141 0.02918 0.01084 0.0072 0.99853 0.97437 0.12264 0.55403 76 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40684 40684 SRR3231275 SRX1637082 SRS1342921 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate2.1 GSM2090848   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090848 GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq GSM2090848   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090848 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate2_R1_001.fastq.gz 24hpf_wt_Plate2_R2_001.fastq.gz fastq fastq 302297329.0 2004669.0 GSM2090848 r4 0:75.44 1:75.35 A:94284770;C:45616868;G:52928512;T:109434957;N:32222 75 75     94284770 45616868 52928512 109434957 32222 SRX1637082 SRS1342921 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01369 0.02852 0.01069 0.00705 0.99874 0.97526 0.10472 0.56414 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40685 40685 SRR3231268 SRX1637081 SRS1342935 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate1.1 GSM2090847   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090847 GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090847   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090847 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate1.1_R1_001.fastq.gz 24hpf_wt_Plate1.1_R2_001.fastq.gz fastq fastq 836011252.0 5542746.0 GSM2090847 r1 0:75.49 1:75.34 A:254663944;C:151442656;G:167697929;T:262199779;N:6944 75 75     254663944 151442656 167697929 262199779 6944 SRX1637081 SRS1342935 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.03375 0.07314 0.02792 0.0396 0.98882 0.95753 0.54559 0.53265 76 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40686 40686 SRR3231269 SRX1637081 SRS1342935 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate1.1 GSM2090847   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090847 GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090847   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090847 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate1.2_R1_001.fastq.gz 24hpf_wt_Plate1.2_R2_001.fastq.gz fastq fastq 830338169.0 5505101.0 GSM2090847 r2 0:75.49 1:75.34 A:254439239;C:150818963;G:164159782;T:260734365;N:185820 75 75     254439239 150818963 164159782 260734365 185820 SRX1637081 SRS1342935 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.03438 0.07482 0.02833 0.04098 0.98867 0.95868 0.55778 0.56233 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40687 40687 SRR3231270 SRX1637081 SRS1342935 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate1.1 GSM2090847   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090847 GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090847   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090847 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate1.3_R1_001.fastq.gz 24hpf_wt_Plate1.3_R2_001.fastq.gz fastq fastq 832999933.0 5522579.0 GSM2090847 r3 0:75.49 1:75.34 A:252395960;C:151022816;G:167338952;T:262031054;N:211151 75 75     252395960 151022816 167338952 262031054 211151 SRX1637081 SRS1342935 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.0331 0.07425 0.02697 0.04008 0.98817 0.95862 0.53915 0.54556 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40688 40688 SRR3231271 SRX1637081 SRS1342935 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf wt Plate1.1 GSM2090847   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf wt Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090847 GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq GSM2090847   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090847 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_wt_Plate1_R1_001.fastq.gz 24hpf_wt_Plate1_R2_001.fastq.gz fastq fastq 838188458.0 5557389.0 GSM2090847 r4 0:75.48 1:75.34 A:257879266;C:152322486;G:165090591;T:262885421;N:10694 75 75     257879266 152322486 165090591 262885421 10694 SRX1637081 SRS1342935 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.03416 0.07497 0.0282 0.04152 0.98871 0.95927 0.49844 0.55123 75 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40689 40689 SRR3231264 SRX1637080 SRS1342936 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate3.1 GSM2090846   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090846 GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq GSM2090846   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz fastq fastq 1371297393.0 9095769.0 GSM2090846 r1 0:75.42 1:75.35 A:425284978;C:236010283;G:260994358;T:448883843;N:123931 75 75     425284978 236010283 260994358 448883843 123931 SRX1637080 SRS1342936 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01833 0.04333 0.01582 0.01601 0.99594 0.96871 0.43243 0.56321 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40690 40690 SRR3231265 SRX1637080 SRS1342936 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate3.1 GSM2090846   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090846 GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq GSM2090846   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz fastq fastq 1397660189.0 9270812.0 GSM2090846 r2 0:75.42 1:75.34 A:435127552;C:240183852;G:263594089;T:458617665;N:137031 75 75     435127552 240183852 263594089 458617665 137031 SRX1637080 SRS1342936 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01782 0.04718 0.01547 0.01691 0.9963 0.96737 0.46382 0.54605 75 76 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40691 40691 SRR3231266 SRX1637080 SRS1342936 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate3.1 GSM2090846   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090846 GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq GSM2090846   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz fastq fastq 1369635087.0 9085243.0 GSM2090846 r3 0:75.41 1:75.34 A:425335498;C:234980221;G:259843705;T:449365378;N:110285 75 75     425335498 234980221 259843705 449365378 110285 SRX1637080 SRS1342936 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01833 0.04405 0.01594 0.01596 0.99636 0.9694 0.49166 0.56044 76 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40692 40692 SRR3231267 SRX1637080 SRS1342936 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate3.1 GSM2090846   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate3.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090846 GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq GSM2090846   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz fastq fastq 1410682920.0 9356966.0 GSM2090846 r4 0:75.42 1:75.34 A:436822225;C:244639009;G:267991531;T:461073192;N:156963 75 75     436822225 244639009 267991531 461073192 156963 SRX1637080 SRS1342936 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.01761 0.04359 0.01513 0.01603 0.99584 0.96871 0.46718 0.55856 75 75 T T mates < 9% mapping rate illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40693 40693 SRR3231260 SRX1637079 SRS1342937 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate2.1 GSM2090845   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090845 GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq GSM2090845   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz fastq fastq 908747232.0 6024927.0 GSM2090845 r1 0:75.47 1:75.36 A:280168278;C:154557506;G:169723057;T:304291004;N:7387 75 75     280168278 154557506 169723057 304291004 7387 SRX1637079 SRS1342937 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.18399 0.33806 0.16099 0.20721 0.95846 0.87878 0.49734 0.53532 76 75 B B mate1-mate2 similar by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40694 40694 SRR3231261 SRX1637079 SRS1342937 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate2.1 GSM2090845   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090845 GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq GSM2090845   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz fastq fastq 899928650.0 5966433.0 GSM2090845 r2 0:75.47 1:75.36 A:279603733;C:153512612;G:165252396;T:301355799;N:204110 75 75     279603733 153512612 165252396 301355799 204110 SRX1637079 SRS1342937 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.18665 0.33654 0.16315 0.20612 0.95812 0.87641 0.48791 0.53087 75 75 B B mate1-mate2 similar by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40695 40695 SRR3231262 SRX1637079 SRS1342937 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate2.1 GSM2090845   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090845 GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq GSM2090845   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz fastq fastq 910589284.0 6036899.0 GSM2090845 r3 0:75.47 1:75.36 A:279344268;C:154985581;G:170329370;T:305702456;N:227609 75 75     279344268 154985581 170329370 305702456 227609 SRX1637079 SRS1342937 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.1847 0.33529 0.16159 0.20809 0.95806 0.88101 0.48203 0.53309 76 75 B B mate1-mate2 similar by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40696 40696 SRR3231263 SRX1637079 SRS1342937 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate2.1 GSM2090845   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate2.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090845 GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq GSM2090845   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz fastq fastq 911364231.0 6042507.0 GSM2090845 r4 0:75.46 1:75.36 A:284483499;C:155490114;G:166537185;T:304841630;N:11803 75 75     284483499 155490114 166537185 304841630 11803 SRX1637079 SRS1342937 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.1873 0.33611 0.16336 0.20573 0.95812 0.87554 0.48685 0.52933 76 76 B B mate1-mate2 similar by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40697 40697 SRR3231256 SRX1637078 SRS1342938 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate1.1 GSM2090844   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090844 GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq GSM2090844   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090844 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz fastq fastq 604973130.0 4010320.0 GSM2090844 r1 0:75.46 1:75.39 A:187609294;C:95230616;G:105121464;T:217006596;N:5160 75 75     187609294 95230616 105121464 217006596 5160 SRX1637078 SRS1342938 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.24179 0.45155 0.21128 0.26362 0.95475 0.84183 0.54132 0.53298 76 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40698 40698 SRR3231257 SRX1637078 SRS1342938 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate1.1 GSM2090844   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090844 GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq GSM2090844   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090844 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz fastq fastq 597266507.0 3959286.0 GSM2090844 r2 0:75.46 1:75.39 A:186751324;C:94261867;G:101806474;T:214309214;N:137628 75 75     186751324 94261867 101806474 214309214 137628 SRX1637078 SRS1342938 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.24002 0.44945 0.20966 0.26222 0.95595 0.84313 0.53005 0.52366 75 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40699 40699 SRR3231258 SRX1637078 SRS1342938 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate1.1 GSM2090844   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090844 GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq GSM2090844   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090844 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz fastq fastq 600809103.0 3982665.0 GSM2090844 r3 0:75.47 1:75.39 A:185579699;C:94586895;G:104466591;T:216021526;N:154392 75 75     185579699 94586895 104466591 216021526 154392 SRX1637078 SRS1342938 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.24004 0.44637 0.21044 0.26336 0.95619 0.84991 0.52752 0.53543 76 76 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40700 40700 SRR3231259 SRX1637078 SRS1342938 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   24hpf Tdrd6a : Plate1.1 GSM2090844   tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 24hpf Tdrd6a : Plate1.1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090844 GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq GSM2090844   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090844 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     24hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz fastq fastq 599838493.0 3976457.0 GSM2090844 r4 0:75.46 1:75.39 A:188491793;C:94714801;G:101689123;T:214934949;N:7827 75 75     188491793 94714801 101689123 214934949 7827 SRX1637078 SRS1342938 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.23905 0.44741 0.2093 0.26277 0.95619 0.84196 0.53501 0.52664 75 75 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Pharyngula Embryo Gonad Reproductive System
40998 40998 SRR3996126 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L001_R2_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L001_R1_001.fastq.gz fastq fastq 122148536.0 803714.0 GSM2258261 r1 0:75.99 1:75.99 A:22296766;C:36021766;G:45626801;T:18125967;N:77236 75 75     22296766 36021766 45626801 18125967 77236 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 1e-05 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
40999 40999 SRR3996127 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L002_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L002_R2_001.fastq.gz fastq fastq 113008241.0 743600.0 GSM2258261 r2 0:75.99 1:75.99 A:20637948;C:33145860;G:42408819;T:16743893;N:71721 75 75     20637948 33145860 42408819 16743893 71721 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 0.00017 0.00998 4e-05 0.00226 0.99967 0.99973 0.72727 0.52941 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41000 41000 SRR3996128 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L003_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L003_R2_001.fastq.gz fastq fastq 108228662.0 712150.0 GSM2258261 r3 0:75.99 1:75.99 A:19849294;C:31892676;G:40324932;T:16132730;N:29030 75 75     19849294 31892676 40324932 16132730 29030 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 2e-05 0.0012 0.0 0.0 0.99995 0.99997 1.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41001 41001 SRR3996129 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L004_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L004_R2_001.fastq.gz fastq fastq 111312836.0 732495.0 GSM2258261 r4 0:75.98 1:75.98 A:20513000;C:32586302;G:41550816;T:16635032;N:27686 75 75     20513000 32586302 41550816 16635032 27686 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 0.00035 0.01956 0.00011 0.00409 0.99953 0.99955 0.69767 0.67647 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41002 41002 SRR3996122 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L001_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L001_R2_001.fastq.gz fastq fastq 108531563.0 714105.0 GSM2258260 r1 0:75.99 1:75.99 A:19184954;C:32230923;G:40631595;T:16417885;N:66206 75 75     19184954 32230923 40631595 16417885 66206 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 3e-05 0.00362 0.0 0.00288 0.99997 0.99997 0.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41003 41003 SRR3996123 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L002_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L002_R2_001.fastq.gz fastq fastq 101227523.0 666088.0 GSM2258260 r2 0:75.98 1:75.99 A:17949430;C:29881418;G:37998433;T:15333962;N:64280 75 75     17949430 29881418 37998433 15333962 64280 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 0.00025 0.01395 5e-05 0.00403 0.99955 0.99959 0.68571 0.74074 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41004 41004 SRR3996124 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L003_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L003_R2_001.fastq.gz fastq fastq 96887228.0 637499.0 GSM2258260 r3 0:75.99 1:75.99 A:17147788;C:28784101;G:36238086;T:14692025;N:25228 75 75     17147788 28784101 36238086 14692025 25228 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 2e-05 0.00088 1e-05 0.0 1.0 0.99997   1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41005 41005 SRR3996125 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L004_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L004_R2_001.fastq.gz fastq fastq 100376357.0 660556.0 GSM2258260 r4 0:75.98 1:75.98 A:17996732;C:29527900;G:37433615;T:15391508;N:26602 75 75     17996732 29527900 37433615 15391508 26602 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 0.00061 0.027 0.0001 0.00825 0.99928 0.99945 0.74444 0.64406 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41010 41010 SRR3536535 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4protein_AHG7CMBGXX_S11_L001_R2_001.fastq.gz fastq 113791000.0 749237.0 GSM2155530 r1 0:75.98 1:75.90 A:20602049;C:33698647;G:40809975;T:18435912;N:244417 75 75     20602049 33698647 40809975 18435912 244417 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41011 41011 SRR3536536 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4protein_AHG7CMBGXX_S11_L002_R1_001.fastq.gz zfGFP4protein_AHG7CMBGXX_S11_L002_R2_001.fastq.gz fastq fastq 114510782.0 753967.0 GSM2155530 r2 0:75.98 1:75.90 A:20684140;C:33805645;G:41313135;T:18471924;N:235938 75 75     20684140 33805645 41313135 18471924 235938 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41012 41012 SRR3536537 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         109968569.0 724055.0 GSM2155530 r3 0:75.98 1:75.90 A:19878654;C:32566435;G:39496562;T:17888872;N:138046 75 75     19878654 32566435 39496562 17888872 138046 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41013 41013 SRR3536538 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         110729697.0 729061.0 GSM2155530 r4 0:75.98 1:75.90 A:19967167;C:32715452;G:39992653;T:17912669;N:141756 75 75     19967167 32715452 39992653 17912669 141756 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 1e-05 1e-05 0.0 0.0 0.99997 0.99997 0.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41014 41014 SRR3536479 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L001_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L001_R2_001.fastq.gz fastq fastq 616561738.0 4058387.0 GSM2155516 r1 0:75.99 1:75.94 A:113223336;C:179378849;G:225550023;T:98403521;N:6009 75 75     113223336 179378849 225550023 98403521 6009 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.0031 0.00224 0.00298 0.00037 0.99997 0.99815 0.0 0.54485 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41015 41015 SRR3536480 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L002_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L002_R2_001.fastq.gz fastq fastq 612631229.0 4032528.0 GSM2155516 r2 0:75.99 1:75.94 A:112250860;C:177589654;G:225470620;T:97316352;N:3743 75 75     112250860 177589654 225470620 97316352 3743 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00328 0.00181 0.00318 0.00027 0.99993 0.99833 0.0 0.5232 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41016 41016 SRR3536481 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L003_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L003_R2_001.fastq.gz fastq fastq 616370738.0 4057190.0 GSM2155516 r3 0:75.99 1:75.93 A:113279678;C:179263048;G:225399046;T:98410557;N:18409 75 75     113279678 179263048 225399046 98410557 18409 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00317 0.00192 0.00306 0.00033 0.99997 0.99827 0.0 0.55294 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41017 41017 SRR3536482 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L004_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L004_R2_001.fastq.gz fastq fastq 624786188.0 4112554.0 GSM2155516 r4 0:75.99 1:75.94 A:114515054;C:181154041;G:229755683;T:99341492;N:19918 75 75     114515054 181154041 229755683 99341492 19918 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00297 0.00211 0.00286 0.00033 0.99997 0.99821 0.0 0.53287 76 75 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41018 41018 SRR3536475 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         648114567.0 4265856.0 GSM2155515 r1 0:75.99 1:75.94 A:117475168;C:188313577;G:240281561;T:102038272;N:5989 75 75     117475168 188313577 240281561 102038272 5989 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 2e-05 2e-05 0.0 0.0 0.99995 0.99997 0.0 0.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41019 41019 SRR3536476 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L002_R1_001.fastq.gz zfGFP4tomo2_AHF5FNBGXX_S8_L002_R2_001.fastq.gz fastq fastq 645912335.0 4251368.0 GSM2155515 r2 0:75.99 1:75.94 A:116787859;C:186995532;G:240912198;T:101212725;N:4021 75 75     116787859 186995532 240912198 101212725 4021 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 3e-05 2e-05 1e-05 1e-05 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41020 41020 SRR3536477 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L003_R1_001.fastq.gz fastq 650554243.0 4281969.0 GSM2155515 r3 0:75.99 1:75.94 A:118039991;C:188970659;G:241065842;T:102458188;N:19563 75 75     118039991 188970659 241065842 102458188 19563 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 2e-05 1e-05 0.0 0.0 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41021 41021 SRR3536478 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L004_R1_001.fastq.gz fastq 657902363.0 4330308.0 GSM2155515 r4 0:75.99 1:75.94 A:119079652;C:190479252;G:245168127;T:103153508;N:21824 75 75     119079652 190479252 245168127 103153508 21824 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 0.0 4e-05 0.0 2e-05 1.0 0.99995   0.5 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
48231 48231 SRR7119834 SRX4041477 SRS3259001 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 9 GSM3131225   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 9 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131225 GSM3131225: Danio rerio RNAseq singleHeart 1dpf mut 9; Danio rerio; RNA Seq GSM3131225   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131225 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_9_NDCII_sample_0023.fastq.gz fastq 57070136.0 762325.0 GSM3131225 r1 0:74.86 A:18605697;C:9652744;G:12793849;T:15973861;N:43985 74       18605697 9652744 12793849 15973861 43985 SRX4041477 SRS3259001 SRA699717 GEO Molecular Biology, Radboud University 1 0.65648   0.53947   0.94448   0.46511   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48232 48232 SRR7119833 SRX4041476 SRS3258954 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 7 GSM3131224   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 7 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131224 GSM3131224: Danio rerio RNAseq singleHeart 1dpf mut 7; Danio rerio; RNA Seq GSM3131224   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131224 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_7_NDCII_sample_0020.fastq.gz fastq 95756013.0 1278688.0 GSM3131224 r1 0:74.89 A:31571219;C:16875591;G:19112888;T:28125288;N:71027 74       31571219 16875591 19112888 28125288 71027 SRX4041476 SRS3258954 SRA699717 GEO Molecular Biology, Radboud University 1 0.77787   0.38573   0.89491   0.52033   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48233 48233 SRR7119832 SRX4041475 SRS3258953 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 6 GSM3131223   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 6 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131223 GSM3131223: Danio rerio RNAseq singleHeart 1dpf mut 6; Danio rerio; RNA Seq GSM3131223   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131223 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_6_NDCII_sample_0019.fastq.gz fastq 42326230.0 565166.0 GSM3131223 r1 0:74.89 A:13786789;C:7205959;G:8673068;T:12629903;N:30511 74       13786789 7205959 8673068 12629903 30511 SRX4041475 SRS3258953 SRA699717 GEO Molecular Biology, Radboud University 1 0.81231   0.24386   0.91662   0.54902   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48234 48234 SRR7119831 SRX4041474 SRS3258952 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 5 GSM3131222   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 5 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131222 GSM3131222: Danio rerio RNAseq singleHeart 1dpf mut 5; Danio rerio; RNA Seq GSM3131222   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131222 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_5_NDCII_sample_0018.fastq.gz fastq 19727283.0 263414.0 GSM3131222 r1 0:74.89 A:6628087;C:3386996;G:3817542;T:5879595;N:15063 74       6628087 3386996 3817542 5879595 15063 SRX4041474 SRS3258952 SRA699717 GEO Molecular Biology, Radboud University 1 0.77937   0.38158   0.93681   0.49785   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48235 48235 SRR7119830 SRX4041473 SRS3258951 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 4 GSM3131221   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 4 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131221 GSM3131221: Danio rerio RNAseq singleHeart 1dpf mut 4; Danio rerio; RNA Seq GSM3131221   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131221 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_4_NDCII_sample_0017.fastq.gz fastq 58279623.0 778471.0 GSM3131221 r1 0:74.86 A:18649049;C:9706373;G:12497900;T:17382327;N:43974 74       18649049 9706373 12497900 17382327 43974 SRX4041473 SRS3258951 SRA699717 GEO Molecular Biology, Radboud University 1 0.7618   0.36032   0.91425   0.50881   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48236 48236 SRR7119829 SRX4041472 SRS3258950 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 3 GSM3131220   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 3 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131220 GSM3131220: Danio rerio RNAseq singleHeart 1dpf mut 3; Danio rerio; RNA Seq GSM3131220   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131220 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_3_NDCII_sample_0016.fastq.gz fastq 76875810.0 1027192.0 GSM3131220 r1 0:74.84 A:25047740;C:13094049;G:17143346;T:21533451;N:57224 74       25047740 13094049 17143346 21533451 57224 SRX4041472 SRS3258950 SRA699717 GEO Molecular Biology, Radboud University 1 0.73765   0.57489   0.91297   0.50116   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48237 48237 SRR7119828 SRX4041471 SRS3258949 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 2 GSM3131219   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 2 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131219 GSM3131219: Danio rerio RNAseq singleHeart 1dpf mut 2; Danio rerio; RNA Seq GSM3131219   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131219 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_2_NDCII_sample_0015.fastq.gz fastq 279841644.0 3736395.0 GSM3131219 r1 0:74.90 A:89952643;C:48371385;G:56655773;T:84653645;N:208198 74       89952643 48371385 56655773 84653645 208198 SRX4041471 SRS3258949 SRA699717 GEO Molecular Biology, Radboud University 1 0.83707   0.16537   0.8449   0.51435   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48238 48238 SRR7119827 SRX4041470 SRS3258948 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf mut 1 GSM3131218   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / Danio rerio RNAseq singleHeart 1dpf mut 1 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / GSM3131218 GSM3131218: Danio rerio RNAseq singleHeart 1dpf mut 1; Danio rerio; RNA Seq GSM3131218   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131218 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     mut_1_1_NDCII_sample_0014.fastq.gz fastq 11439626.0 152750.0 GSM3131218 r1 0:74.89 A:3900812;C:1903149;G:2137242;T:3490826;N:7597 74       3900812 1903149 2137242 3490826 7597 SRX4041470 SRS3258948 SRA699717 GEO Molecular Biology, Radboud University 1 0.81522   0.22036   0.9427   0.50565   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48239 48239 SRR7119826 SRX4041469 SRS3258947 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 11 GSM3131217   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 11 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131217 GSM3131217: Danio rerio RNAseq singleHeart 1dpf wt 11; Danio rerio; RNA Seq GSM3131217   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131217 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_11_NDCII_sample_0013.fastq.gz fastq 42251524.0 564309.0 GSM3131217 r1 0:74.87 A:13857230;C:6932231;G:9360286;T:12071859;N:29918 74       13857230 6932231 9360286 12071859 29918 SRX4041469 SRS3258947 SRA699717 GEO Molecular Biology, Radboud University 1 0.73137   0.44634   0.93196   0.46969   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48240 48240 SRR7119825 SRX4041468 SRS3258946 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 9 GSM3131216   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 9 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131216 GSM3131216: Danio rerio RNAseq singleHeart 1dpf wt 9; Danio rerio; RNA Seq GSM3131216   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131216 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_9_NDCII_sample_0010.fastq.gz fastq 140217783.0 1872511.0 GSM3131216 r1 0:74.88 A:48060012;C:23208078;G:28722039;T:40121038;N:106616 74       48060012 23208078 28722039 40121038 106616 SRX4041468 SRS3258946 SRA699717 GEO Molecular Biology, Radboud University 1 0.80665   0.32237   0.86778   0.52038   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48241 48241 SRR7119824 SRX4041467 SRS3258945 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 7 GSM3131215   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 7 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131215 GSM3131215: Danio rerio RNAseq singleHeart 1dpf wt 7; Danio rerio; RNA Seq GSM3131215   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131215 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_7_NDCII_sample_0008.fastq.gz fastq 23549291.0 314631.0 GSM3131215 r1 0:74.85 A:8015580;C:3998401;G:4892477;T:6623855;N:18978 74       8015580 3998401 4892477 6623855 18978 SRX4041467 SRS3258945 SRA699717 GEO Molecular Biology, Radboud University 1 0.71017   0.48929   0.94817   0.56724   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48242 48242 SRR7119823 SRX4041466 SRS3258944 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 6 GSM3131214   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 6 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131214 GSM3131214: Danio rerio RNAseq singleHeart 1dpf wt 6; Danio rerio; RNA Seq GSM3131214   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131214 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_6_NDCII_sample_0007.fastq.gz fastq 129689911.0 1732243.0 GSM3131214 r1 0:74.87 A:40869250;C:21297938;G:30638559;T:36786070;N:98094 74       40869250 21297938 30638559 36786070 98094 SRX4041466 SRS3258944 SRA699717 GEO Molecular Biology, Radboud University 1 0.77101   0.59088   0.88824   0.5086   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48243 48243 SRR7119822 SRX4041465 SRS3258943 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 5 GSM3131213   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 5 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131213 GSM3131213: Danio rerio RNAseq singleHeart 1dpf wt 5; Danio rerio; RNA Seq GSM3131213   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131213 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_5_NDCII_sample_0006.fastq.gz fastq 24218974.0 323441.0 GSM3131213 r1 0:74.88 A:8220059;C:3989695;G:4906493;T:7085365;N:17362 74       8220059 3989695 4906493 7085365 17362 SRX4041465 SRS3258943 SRA699717 GEO Molecular Biology, Radboud University 1 0.76586   0.49207   0.93501   0.55288   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48244 48244 SRR7119821 SRX4041464 SRS3258942 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 4 GSM3131212   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 4 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131212 GSM3131212: Danio rerio RNAseq singleHeart 1dpf wt 4; Danio rerio; RNA Seq GSM3131212   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131212 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_4_NDCII_sample_0005.fastq.gz fastq 22001311.0 293804.0 GSM3131212 r1 0:74.88 A:7350666;C:3795843;G:4584903;T:6252967;N:16932 74       7350666 3795843 4584903 6252967 16932 SRX4041464 SRS3258942 SRA699717 GEO Molecular Biology, Radboud University 1 0.7875   0.22891   0.93835   0.52263   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48245 48245 SRR7119820 SRX4041463 SRS3258941 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 3 GSM3131211   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 3 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131211 GSM3131211: Danio rerio RNAseq singleHeart 1dpf wt 3; Danio rerio; RNA Seq GSM3131211   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131211 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_3_NDCII_sample_0004.fastq.gz fastq 113079916.0 1510783.0 GSM3131211 r1 0:74.85 A:37699535;C:19622685;G:23847263;T:31822581;N:87852 74       37699535 19622685 23847263 31822581 87852 SRX4041463 SRS3258941 SRA699717 GEO Molecular Biology, Radboud University 1 0.76704   0.49567   0.89045   0.51015   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48246 48246 SRR7119819 SRX4041462 SRS3258977 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 2 GSM3131210   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 2 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131210 GSM3131210: Danio rerio RNAseq singleHeart 1dpf wt 2; Danio rerio; RNA Seq GSM3131210   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131210 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_2_NDCII_sample_0003.fastq.gz fastq 28758160.0 384087.0 GSM3131210 r1 0:74.87 A:9200574;C:4647591;G:6808365;T:8081607;N:20023 74       9200574 4647591 6808365 8081607 20023 SRX4041462 SRS3258977 SRA699717 GEO Molecular Biology, Radboud University 1 0.749   0.43154   0.92498   0.50112   74   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
48247 48247 SRR7119818 SRX4041461 SRS3258961 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq singleHeart 1dpf wt 1 GSM3131209   tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ Danio rerio RNAseq singleHeart 1dpf wt 1 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format heart   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+ GSM3131209 GSM3131209: Danio rerio RNAseq singleHeart 1dpf wt 1; Danio rerio; RNA Seq GSM3131209   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131209 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP144601     W_1_1_NDCII_sample_0002.fastq.gz fastq 115972945.0 1548390.0 GSM3131209 r1 0:74.90 A:39437412;C:19997472;G:22424748;T:34023469;N:89844 74       39437412 19997472 22424748 34023469 89844 SRX4041461 SRS3258961 SRA699717 GEO Molecular Biology, Radboud University 1 0.81745   0.22051   0.87746   0.55768   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Pharyngula Embryo Heart Cardiovascular System
51311 51311 SRR8732849 SRX5525702 SRS4492378 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis GSM3672158   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672158 GSM3672158: Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis; Danio rerio; RNA Seq GSM3672158   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672158 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample17_R1_zcat.fastq.gz Sample17_R2_zcat.fastq.gz fastq fastq 8156614941.0 54091984.0 GSM3672158 r1 0:75.34 1:75.45 A:2414004672;C:1132746308;G:1388606792;T:3220760873;N:496296 75 75     2414004672 1132746308 1388606792 3220760873 496296 SRX5525702 SRS4492378 SRA860716 GEO Hubrecht Institute 2 0.0447 0.79211 0.03174 0.19541 0.99622 0.84413 0.42608 0.54026 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51312 51312 SRR8732848 SRX5525701 SRS4492377 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis GSM3672157   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf GSM3672157 GSM3672157: Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672157   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672157 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample15_R1_zcat.fastq.gz Sample15_R2_zcat.fastq.gz fastq fastq 6313331656.0 41861859.0 GSM3672157 r1 0:75.35 1:75.46 A:1835394541;C:855041539;G:1018382135;T:2604142980;N:370461 75 75     1835394541 855041539 1018382135 2604142980 370461 SRX5525701 SRS4492377 SRA860716 GEO Hubrecht Institute 2 0.05321 0.82346 0.04331 0.23083 0.99786 0.83345 0.40714 0.54319 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51313 51313 SRR8732840 SRX5525693 SRS4492370 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis GSM3672149   source name:Dissected trunk|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:40 hpf Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. Dissected trunk   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:40 hpf GSM3672149 GSM3672149: Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis; Danio rerio; RNA Seq GSM3672149   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672149 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample6_R1_zcat.fastq.gz Sample6_R2_zcat.fastq.gz fastq fastq 5587592853.0 37062063.0 GSM3672149 r1 0:75.36 1:75.41 A:1734543706;C:744561818;G:859917019;T:2246189990;N:2380320 75 75     1734543706 744561818 859917019 2246189990 2380320 SRX5525693 SRS4492370 SRA860716 GEO Hubrecht Institute 2 0.0668 0.83117 0.05405 0.29997 0.99669 0.90299 0.45595 0.48918 75 75 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51314 51314 SRR8732839 SRX5525692 SRS4492369 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis GSM3672148   source name:Dissected trunk|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:28 hpf Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. Dissected trunk   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:28 hpf GSM3672148 GSM3672148: Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis; Danio rerio; RNA Seq GSM3672148   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672148 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample5_R1_zcat.fastq.gz Sample5_R2_zcat.fastq.gz fastq fastq 5347713824.0 35489697.0 GSM3672148 r1 0:75.32 1:75.36 A:1730992334;C:750666631;G:941260179;T:1922636857;N:2157823 75 75     1730992334 750666631 941260179 1922636857 2157823 SRX5525692 SRS4492369 SRA860716 GEO Hubrecht Institute 2 0.02738 0.73853 0.02205 0.35749 0.99774 0.93188 0.50877 0.56198 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51315 51315 SRR8732838 SRX5525691 SRS4492367 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis GSM3672147   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672147 GSM3672147: Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672147   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672147 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample4_R2_zcat.fastq.gz Sample4_R1_zcat.fastq.gz fastq fastq 5574969530.0 36993436.0 GSM3672147 r1 0:75.32 1:75.38 A:1776560856;C:755982699;G:888659557;T:2151535116;N:2231302 75 75     1776560856 755982699 888659557 2151535116 2231302 SRX5525691 SRS4492367 SRA860716 GEO Hubrecht Institute 2 0.02327 0.77704 0.01701 0.20977 0.99791 0.89873 0.40944 0.50295 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51316 51316 SRR8732837 SRX5525690 SRS4492365 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis GSM3672146   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672146 GSM3672146: Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672146   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672146 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample2_R2_zcat.fastq.gz Sample2_R1_zcat.fastq.gz fastq fastq 7138373773.0 47379140.0 GSM3672146 r1 0:75.32 1:75.34 A:2341329013;C:975718419;G:1157227064;T:2661209213;N:2890064 75 75     2341329013 975718419 1157227064 2661209213 2890064 SRX5525690 SRS4492365 SRA860716 GEO Hubrecht Institute 2 0.01395 0.71038 0.00951 0.19462 0.99835 0.91056 0.44 0.55129 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51317 51317 SRR8732836 SRX5525689 SRS4492366 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis GSM3672145   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf GSM3672145 GSM3672145: Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672145   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672145 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample1_R1_zcat.fastq.gz Sample1_R2_zcat.fastq.gz fastq fastq 5326304022.0 35338371.0 GSM3672145 r1 0:75.34 1:75.39 A:1700388888;C:661186330;G:779653520;T:2182932216;N:2143068 75 75     1700388888 661186330 779653520 2182932216 2143068 SRX5525689 SRS4492366 SRA860716 GEO Hubrecht Institute 2 0.03106 0.82256 0.02777 0.13469 0.99943 0.8957 0.61538 0.5437 75 75 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
62031 62031 SRR13115057 SRX9557270 SRS7765052 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 4 cdh17 GSM4930029   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 4 cdh17 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930029 GSM4930029: ZNC Day1 4 cdh17; Danio rerio; RNA Seq GSM4930029   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930029 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_4_Cdh17_R1.fastq.gz ZNC_Day1_4_Cdh17_R2.fastq.gz fastq fastq 2620130250.0 17467535.0 GSM4930029 r1 0:75 1:75 A:586017099;C:400844453;G:419358801;T:1213892274;N:17623 75 75     586017099 400844453 419358801 1213892274 17623 SRX9557270 SRS7765052 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.20536 0.8052 0.14853 0.34732 0.9918 0.80466 0.12586 0.67366 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62032 62032 SRR13115056 SRX9557269 SRS7758083 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 4 GSM4930028   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 4 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930028 GSM4930028: ZNC Day1 4; Danio rerio; RNA Seq GSM4930028   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930028 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_4_R1.fastq.gz ZNC_Day1_4_R2.fastq.gz fastq fastq 1824990500.0 18249905.0 GSM4930028 r1 0:30 1:70 A:473976672;C:320918108;G:324168670;T:705832460;N:94590 30 70     473976672 320918108 324168670 705832460 94590 SRX9557269 SRS7758083 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.44709 0.76785 0.42343 0.45478 0.98894 0.82479 0.8491 0.78301 30 70 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62033 62033 SRR13115055 SRX9557268 SRS7764288 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 3 cdh17 GSM4930027   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 3 cdh17 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930027 GSM4930027: ZNC Day1 3 cdh17; Danio rerio; RNA Seq GSM4930027   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930027 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_3_Cdh17_R1.fastq.gz ZNC_Day1_3_Cdh17_R2.fastq.gz fastq fastq 2466426750.0 16442845.0 GSM4930027 r1 0:75 1:75 A:559197003;C:370596624;G:396798736;T:1139817899;N:16488 75 75     559197003 370596624 396798736 1139817899 16488 SRX9557268 SRS7764288 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.17575 0.7187 0.13208 0.34663 0.9918 0.80296 0.13918 0.68008 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62034 62034 SRR13115054 SRX9557267 SRS7774800 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 3 GSM4930026   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 3 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930026 GSM4930026: ZNC Day1 3; Danio rerio; RNA Seq GSM4930026   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930026 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_3_R1.fastq.gz ZNC_Day1_3_R2.fastq.gz fastq fastq 1440247000.0 14402470.0 GSM4930026 r1 0:30 1:70 A:379463608;C:250428466;G:257147695;T:553131395;N:75836 30 70     379463608 250428466 257147695 553131395 75836 SRX9557267 SRS7774800 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.53596 0.7764 0.50896 0.41848 0.99015 0.8294 0.73219 0.81152 30 70 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62035 62035 SRR13115053 SRX9557266 SRS7768946 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 2 cdh17 GSM4930025   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 2 cdh17 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930025 GSM4930025: ZNC Day1 2 cdh17; Danio rerio; RNA Seq GSM4930025   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930025 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_2_Cdh17_R1.fastq.gz ZNC_Day1_2_Cdh17_R2.fastq.gz fastq fastq 3627307650.0 24182051.0 GSM4930025 r1 0:75 1:75 A:815949074;C:553523601;G:584584461;T:1673224749;N:25765 75 75     815949074 553523601 584584461 1673224749 25765 SRX9557266 SRS7768946 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.1809 0.7971 0.13159 0.32692 0.99145 0.79912 0.15023 0.70213 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62036 62036 SRR13115052 SRX9557265 SRS7758099 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 2 GSM4930024   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 2 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930024 GSM4930024: ZNC Day1 2; Danio rerio; RNA Seq GSM4930024   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930024 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_2_R1.fastq.gz ZNC_Day1_2_R2.fastq.gz fastq fastq 1672787100.0 16727871.0 GSM4930024 r1 0:30 1:70 A:440596558;C:289991094;G:295797683;T:646312700;N:89065 30 70     440596558 289991094 295797683 646312700 89065 SRX9557265 SRS7758099 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.45459 0.7826 0.43209 0.43388 0.9904 0.82471 0.7902 0.78112 30 70 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62037 62037 SRR13115051 SRX9557264 SRS7760515 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 1 cdh17 GSM4930023   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 1 cdh17 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930023 GSM4930023: ZNC Day1 1 cdh17; Danio rerio; RNA Seq GSM4930023   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930023 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_1_Cdh17_R1.fastq.gz ZNC_Day1_1_Cdh17_R2.fastq.gz fastq fastq 4232535600.0 28216904.0 GSM4930023 r1 0:75 1:75 A:1022792924;C:659843704;G:675423200;T:1874448065;N:27707 75 75     1022792924 659843704 675423200 1874448065 27707 SRX9557264 SRS7760515 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.17373 0.7926 0.12679 0.32535 0.99354 0.8173 0.15579 0.70536 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62038 62038 SRR13115050 SRX9557263 SRS7763051 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC Day1 1 GSM4930022   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC Day1 1 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930022 GSM4930022: ZNC Day1 1; Danio rerio; RNA Seq GSM4930022   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930022 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_Day1_1_R1.fastq.gz ZNC_Day1_1_R2.fastq.gz fastq fastq 1468134100.0 14681341.0 GSM4930022 r1 0:30 1:70 A:390964306;C:252762227;G:257246886;T:567090777;N:69904 30 70     390964306 252762227 257246886 567090777 69904 SRX9557263 SRS7763051 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.56006 0.77137 0.5273 0.44146 0.99174 0.848 0.49817 0.83793 30 70 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62043 62043 SRR13115045 SRX9557258 SRS7776278 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC D1CTRL 12 GSM4930017   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC D1CTRL 12 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930017 GSM4930017: ZNC D1CTRL 12; Danio rerio; RNA Seq GSM4930017   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930017 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_D1CTRL_12_R1.fastq.gz ZNC_D1CTRL_12_R2.fastq.gz fastq fastq 1457792400.0 9718616.0 GSM4930017 r1 0:75 1:75 A:349174227;C:232621187;G:241864815;T:634073664;N:58507 75 75     349174227 232621187 241864815 634073664 58507 SRX9557258 SRS7776278 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.18225 0.76763 0.14946 0.4049 0.98675 0.81542 0.28298 0.74865 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62044 62044 SRR13115044 SRX9557257 SRS7761371 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC D1CTRL 11 GSM4930016   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC D1CTRL 11 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930016 GSM4930016: ZNC D1CTRL 11; Danio rerio; RNA Seq GSM4930016   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930016 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_D1CTRL_11_R1.fastq.gz ZNC_D1CTRL_11_R2.fastq.gz fastq fastq 1275600900.0 8504006.0 GSM4930016 r1 0:75 1:75 A:309632828;C:204670391;G:213219831;T:548026269;N:51581 75 75     309632828 204670391 213219831 548026269 51581 SRX9557257 SRS7761371 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.17103 0.79111 0.14016 0.382 0.98894 0.83642 0.25652 0.8477 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62045 62045 SRR13115043 SRX9557256 SRS7769436 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC D1CTRL 10 GSM4930015   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC D1CTRL 10 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930015 GSM4930015: ZNC D1CTRL 10; Danio rerio; RNA Seq GSM4930015   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930015 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_D1CTRL_10_R1.fastq.gz ZNC_D1CTRL_10_R2.fastq.gz fastq fastq 1494934050.0 9966227.0 GSM4930015 r1 0:75 1:75 A:363970280;C:238228840;G:251555894;T:641119576;N:59460 75 75     363970280 238228840 251555894 641119576 59460 SRX9557256 SRS7769436 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.16854 0.77932 0.13778 0.38024 0.98831 0.84196 0.24756 0.85074 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
62046 62046 SRR13115042 SRX9557255 SRS7772881 SRP293760 PRJNA680334 Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development GSE162031 Transcriptome Analysis Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.   pubmed:33749326   ZNC D1CTRL 9 GSM4930014   source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf ZNC D1CTRL 9 For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts. Pronephros The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing. Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf GSM4930014 GSM4930014: ZNC D1CTRL 9; Danio rerio; RNA Seq GSM4930014   1 Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol GEO Accession:GSM4930014 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP293760     ZNC_D1CTRL_9_R1.fastq.gz ZNC_D1CTRL_9_R2.fastq.gz fastq fastq 2036209050.0 13574727.0 GSM4930014 r1 0:75 1:75 A:488914558;C:324238359;G:344606252;T:878368742;N:81139 75 75     488914558 324238359 344606252 878368742 81139 SRX9557255 SRS7772881 SRA1162774 GEO Renal Division, Department of Medicine, University Freiburg Medical Center 2 0.16946 0.77979 0.1365 0.39627 0.98853 0.81903 0.21231 0.814 75 75 T B mate1 technical by mapping diff illumina hiseq_era unknown small_rna trueseq sc single_cell_plate celseq   Germany 2020-11-23 Pharyngula Embryo Embryo Imprecise All anatomical structures
63260 63260 SRR13724987 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L001_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L001_R2_001.fastq.gz fastq fastq 724015252.0 8418782.0 GSM5087790 r1 0:26 1:60 A:181448033;C:140181369;G:139987828;T:262155531;N:242491 26 60     181448033 140181369 139987828 262155531 242491 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10352 0.78777 0.09808 0.22696 0.99078 0.81389 0.60135 0.52625 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63261 63261 SRR13724988 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L002_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L002_R2_001.fastq.gz fastq fastq 710763770.0 8264695.0 GSM5087790 r2 0:26 1:60 A:177328072;C:137060064;G:139543912;T:256619367;N:212355 26 60     177328072 137060064 139543912 256619367 212355 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10309 0.78735 0.09769 0.22712 0.9907 0.81434 0.59399 0.51403 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63262 63262 SRR13724989 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L003_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L003_R2_001.fastq.gz fastq fastq 733552222.0 8529677.0 GSM5087790 r3 0:26 1:60 A:183770046;C:141936571;G:141851405;T:265713964;N:280236 26 60     183770046 141936571 141851405 265713964 280236 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10305 0.78993 0.0974 0.22773 0.99058 0.81477 0.59145 0.52341 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63263 63263 SRR13724990 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L004_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L004_R2_001.fastq.gz fastq fastq 721320614.0 8387449.0 GSM5087790 r4 0:26 1:60 A:179946156;C:139058546;G:141752407;T:260320288;N:243217 26 60     179946156 139058546 141752407 260320288 243217 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10209 0.7864 0.09672 0.22655 0.99088 0.81688 0.56585 0.52923 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;