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467 rows where devstage_curation = "Gastrula" and technology = "smartseq"

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  • smartseq · 467 ✖

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  • Gastrula · 467 ✖
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
29202 29202 SRR27329257 SRX23006269 SRS19970080 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Lateral Ectoderm 7.5 hpf 4 GSM7989708   source name:Lateral Ectoderm|tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Lateral Ectoderm 7.5 hpf 4 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Lateral Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989708 GSM7989708: Zebrafish Lateral Ectoderm 7.5 hpf 4; Danio rerio; RNA Seq GSM7989708 r1 GSM7989708 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Lateral_Ectoderm_4.mate1.fastq.gz Lateral_Ectoderm_4.mate2.fastq.gz fastq fastq 6211000588.0 26929501.0 GSM7989708 r1 0:80.64 1:150 A:1950010947;C:1101223011;G:1497556265;T:1656016608;N:6193757 80 150     1950010947 1101223011 1497556265 1656016608 6193757 SRX23006269 SRS19970080 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.65918 0.4633 0.04875 0.02201 0.90623 0.92608 0.79936 0.77887 68 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29203 29203 SRR27329258 SRX23006268 SRS19970081 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Lateral Ectoderm 7.5 hpf 3 GSM7989707   source name:Lateral Ectoderm|tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Lateral Ectoderm 7.5 hpf 3 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Lateral Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989707 GSM7989707: Zebrafish Lateral Ectoderm 7.5 hpf 3; Danio rerio; RNA Seq GSM7989707 r1 GSM7989707 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Lateral_Ectoderm_3.mate1.fastq.gz Lateral_Ectoderm_3.mate2.fastq.gz fastq fastq 5066130338.0 22014930.0 GSM7989707 r1 0:80.12 1:150 A:1476750755;C:934859886;G:1246347548;T:1403280136;N:4892013 80 150     1476750755 934859886 1246347548 1403280136 4892013 SRX23006268 SRS19970081 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.7566 0.52272 0.0462 0.02684 0.89489 0.91246 0.78848 0.77633 68 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29204 29204 SRR27329259 SRX23006267 SRS19970078 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Lateral Ectoderm 7.5 hpf 2 GSM7989706   source name:Lateral Ectoderm|tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Lateral Ectoderm 7.5 hpf 2 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Lateral Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989706 GSM7989706: Zebrafish Lateral Ectoderm 7.5 hpf 2; Danio rerio; RNA Seq GSM7989706 r1 GSM7989706 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Lateral_Ectoderm_2.mate1.fastq.gz Lateral_Ectoderm_2.mate2.fastq.gz fastq fastq 6372234032.0 27787436.0 GSM7989706 r1 0:79.32 1:150 A:1908123129;C:1195826989;G:1555786583;T:1706205499;N:6291832 79 150     1908123129 1195826989 1555786583 1706205499 6291832 SRX23006267 SRS19970078 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.52417 0.50653 0.02922 0.02493 0.89479 0.90938 0.74721 0.74563 68 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29205 29205 SRR27329260 SRX23006266 SRS19970079 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Lateral Ectoderm 7.5 hpf 1 GSM7989705   source name:Lateral Ectoderm|tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Lateral Ectoderm 7.5 hpf 1 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Lateral Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Lateral Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989705 GSM7989705: Zebrafish Lateral Ectoderm 7.5 hpf 1; Danio rerio; RNA Seq GSM7989705 r1 GSM7989705 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Lateral_Ectoderm_1.mate2.fastq.gz Lateral_Ectoderm_1.mate1.fastq.gz fastq fastq 10106832046.0 43799441.0 GSM7989705 r1 0:80.75 1:150 A:3384386532;C:1698196797;G:2308026869;T:2706071735;N:10150113 80 150     3384386532 1698196797 2308026869 2706071735 10150113 SRX23006266 SRS19970079 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.64457 0.42542 0.04802 0.01964 0.91541 0.93878 0.83455 0.83564 68 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29206 29206 SRR27329261 SRX23006265 SRS19970077 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Animal Ectoderm 7.5 hpf 4 GSM7989704   source name:Animal Ectoderm|tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Animal Ectoderm 7.5 hpf 4 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Animal Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989704 GSM7989704: Zebrafish Animal Ectoderm 7.5 hpf 4; Danio rerio; RNA Seq GSM7989704 r1 GSM7989704 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Animal_Ectoderm_4.mate1.fastq.gz Animal_Ectoderm_4.mate2.fastq.gz fastq fastq 5882974802.0 25612144.0 GSM7989704 r1 0:79.69 1:150.00 A:1784390197;C:1112846767;G:1392719296;T:1587227818;N:5790724 79 150     1784390197 1112846767 1392719296 1587227818 5790724 SRX23006265 SRS19970077 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.72169 0.51947 0.04749 0.0244 0.89061 0.91007 0.76259 0.75355 90 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29207 29207 SRR27329262 SRX23006264 SRS19970076 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Animal Ectoderm 7.5 hpf 3 GSM7989703   source name:Animal Ectoderm|tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Animal Ectoderm 7.5 hpf 3 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Animal Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989703 GSM7989703: Zebrafish Animal Ectoderm 7.5 hpf 3; Danio rerio; RNA Seq GSM7989703 r1 GSM7989703 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Animal_Ectoderm_3.mate1.fastq.gz Animal_Ectoderm_3.mate2.fastq.gz fastq fastq 6802628678.0 29741168.0 GSM7989703 r1 0:78.73 1:150 A:1935418861;C:1362666541;G:1651315180;T:1846520380;N:6707716 78 150     1935418861 1362666541 1651315180 1846520380 6707716 SRX23006264 SRS19970076 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.74265 0.48713 0.04983 0.02636 0.87771 0.90335 0.72388 0.71557 68 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29208 29208 SRR27329263 SRX23006263 SRS19970075 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Animal Ectoderm 7.5 hpf 2 GSM7989702   source name:Animal Ectoderm|tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Animal Ectoderm 7.5 hpf 2 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Animal Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989702 GSM7989702: Zebrafish Animal Ectoderm 7.5 hpf 2; Danio rerio; RNA Seq GSM7989702 r1 GSM7989702 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Animal_Ectoderm_2.mate1.fastq.gz Animal_Ectoderm_2.mate2.fastq.gz fastq fastq 6083410864.0 26183986.0 GSM7989702 r1 0:82.33 1:150 A:1976903262;C:1110974120;G:1376486325;T:1613990197;N:5056960 82 150     1976903262 1110974120 1376486325 1613990197 5056960 SRX23006263 SRS19970075 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.73078 0.55778 0.04052 0.02684 0.89509 0.91106 0.77391 0.7649 68 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
29209 29209 SRR27329264 SRX23006262 SRS19970074 SRP479683 PRJNA1055904 BMP dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation GSE251904 Transcriptome Analysis Cell migration is a fundamental process during embryonic development. Most studies in vivo have focussed on the migration of cells using the extracellular matrix ECM as their substrate for migration. In contrast much less is known about how cells migrate on other cells as found in early embryos when the ECM has not yet formed. Here we show that lateral mesendoderm LME cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal pole directed migration of LME cells while the ectoderm at the animal pole halts it. These differences in the permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm a property controlled by BMP signalling within the ectoderm. Collectively these findings identify ectoderm tissue cohesion as one critical factor regulating LME migration during zebrafish gastrulation. Overall design: To investigate the differences in gene expression between animal and lateral ectoderm causing the difference in material properties between the two ectodermal tissues.   pubmed:40057955   Zebrafish Animal Ectoderm 7.5 hpf 1 GSM7989701   source name:Animal Ectoderm|tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS|geo loc name:missing|collection date:missing Zebrafish Animal Ectoderm 7.5 hpf 1 FastQC quality control Trimmomatic adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19 FastQC controlling trimming results salmon Alignment; used flags: seqBias qcBias R DESeq2 differential gene expression analysis; DESEq2 apeglm tximport genefilter GenomicRanges R EnhancedVolcano & biomaRt visualization Assembly: Danio rerio GRCz11 Supplementary files format and content: tab delimited text file with gene name gene length effective length tpm and number of reads for each sample Animal Ectoderm Embryo were injected with 125 pg of PAmCherry1 mRNA at xxx cell stage. At 6 hpf embryos were mounted for up right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. post photoactivation embryos were transferred in Ca2+ free Ringer solution and dissociated by gently pipetting using a P 1000 pipette to obtain a single cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer RNeasy Plus Micro Kit QIAGEN with 1% of 2 mercaptoethanol. Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems. Embryos were kept at 28.5 C until dissociation tissue:Animal Ectoderm|genotype:WT TgSebox::eGFP embryos|treatment:1 cell stage injection of PAmCherry1 mRNA Photoactivation FACS GSM7989701 GSM7989701: Zebrafish Animal Ectoderm 7.5 hpf 1; Danio rerio; RNA Seq GSM7989701 r1 GSM7989701 1 Cells were subjected to RNA extraction using RNeasy Plus Micro Kit QIAGEN according to the manufacturer instructions Complete cDNA synthesis and library preparation were performed using SMART Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR KAPA Biosysytems.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479683     Animal_Ectoderm_1.mate1.fastq.gz Animal_Ectoderm_1.mate2.fastq.gz fastq fastq 7195859200.0 31306406.0 GSM7989701 r1 0:79.85 1:150 A:2025250331;C:1450062111;G:1771726396;T:1941745747;N:7074615 79 150     2025250331 1450062111 1771726396 1941745747 7074615 SRX23006262 SRS19970074 SRA1774740 Heisenberg group, Institute of Science and Technology Austria (ISTA) Heisenberg group, Institute of Science and Technology Austria (ISTA) 2 0.74201 0.52197 0.04312 0.02595 0.87941 0.9013 0.74298 0.71509 68 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Austria 2023-12-22 Gastrula Embryo Embryo Imprecise All anatomical structures
44076 44076 SRR6250374 SRX3357301 SRS2656385 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S9 GSM2838460   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S9 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838460 GSM2838460: wt p4 S9; Danio rerio; RNA Seq GSM2838460   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S9.R1.fastq.gz wt_p4_S9.R2.fastq.gz fastq fastq 61039160.0 1089985.0 GSM2838460 r1 0:24 1:32 A:16411881;C:13934629;G:14159762;T:16484450;N:48438 24 32     16411881 13934629 14159762 16484450 48438 SRX3357301 SRS2656385 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77476 0.82366 0.12876 0.13588 0.85766 0.85774 0.72622 0.72762 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44077 44077 SRR6250373 SRX3357300 SRS2656381 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S8 GSM2838459   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S8 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838459 GSM2838459: wt p4 S8; Danio rerio; RNA Seq GSM2838459   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S8.R1.fastq.gz wt_p4_S8.R2.fastq.gz fastq fastq 3221400.0 57525.0 GSM2838459 r1 0:24 1:32 A:857299;C:737999;G:752784;T:870887;N:2431 24 32     857299 737999 752784 870887 2431 SRX3357300 SRS2656381 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76405 0.81832 0.15327 0.16586 0.90983 0.90826 0.73965 0.74051 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44078 44078 SRR6250372 SRX3357299 SRS2656383 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S7 GSM2838458   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S7 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838458 GSM2838458: wt p4 S7; Danio rerio; RNA Seq GSM2838458   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S7.R1.fastq.gz wt_p4_S7.R2.fastq.gz fastq fastq 61365472.0 1095812.0 GSM2838458 r1 0:24 1:32 A:16777185;C:13827520;G:13996928;T:16714262;N:49577 24 32     16777185 13827520 13996928 16714262 49577 SRX3357299 SRS2656383 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78049 0.82981 0.09421 0.09809 0.8579 0.85882 0.74187 0.74992 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44079 44079 SRR6250371 SRX3357298 SRS2656380 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S6 GSM2838457   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S6 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838457 GSM2838457: wt p4 S6; Danio rerio; RNA Seq GSM2838457   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S6.R1.fastq.gz wt_p4_S6.R2.fastq.gz fastq fastq 70813008.0 1264518.0 GSM2838457 r1 0:24 1:32 A:18473405;C:16677041;G:16946924;T:18657517;N:58121 24 32     18473405 16677041 16946924 18657517 58121 SRX3357298 SRS2656380 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78649 0.83922 0.17937 0.19426 0.84656 0.84713 0.69099 0.68701 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44080 44080 SRR6250370 SRX3357296 SRS2656379 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S5 GSM2838456   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S5 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838456 GSM2838456: wt p4 S5; Danio rerio; RNA Seq GSM2838456   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S5.R1.fastq.gz wt_p4_S5.R2.fastq.gz fastq fastq 73596656.0 1314226.0 GSM2838456 r1 0:24 1:32 A:18627101;C:17852449;G:18124666;T:18933645;N:58795 24 32     18627101 17852449 18124666 18933645 58795 SRX3357296 SRS2656379 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78607 0.84024 0.21328 0.23201 0.85543 0.85405 0.69857 0.70151 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44081 44081 SRR6250369 SRX3357295 SRS2656377 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S4 GSM2838455   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S4 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838455 GSM2838455: wt p4 S4; Danio rerio; RNA Seq GSM2838455   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S4.R2.fastq.gz wt_p4_S4.R1.fastq.gz fastq fastq 3035032.0 54197.0 GSM2838455 r1 0:24 1:32 A:827352;C:678981;G:690970;T:835185;N:2544 24 32     827352 678981 690970 835185 2544 SRX3357295 SRS2656377 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77706 0.82883 0.10498 0.11133 0.90701 0.90603 0.75427 0.76069 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44082 44082 SRR6250368 SRX3357294 SRS2656376 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S3 GSM2838454   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S3 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838454 GSM2838454: wt p4 S3; Danio rerio; RNA Seq GSM2838454   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S3.R1.fastq.gz wt_p4_S3.R2.fastq.gz fastq fastq 74236232.0 1325647.0 GSM2838454 r1 0:24 1:32 A:20239486;C:16647872;G:16937826;T:20349461;N:61587 24 32     20239486 16647872 16937826 20349461 61587 SRX3357294 SRS2656376 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77839 0.83033 0.13135 0.1391 0.84338 0.8437 0.70804 0.71279 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44083 44083 SRR6250367 SRX3357293 SRS2656374 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S2 GSM2838453   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S2 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838453 GSM2838453: wt p4 S2; Danio rerio; RNA Seq GSM2838453   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S2.R1.fastq.gz wt_p4_S2.R2.fastq.gz fastq fastq 75103448.0 1341133.0 GSM2838453 r1 0:24 1:32 A:19864937;C:17468556;G:17687706;T:20021624;N:60625 24 32     19864937 17468556 17687706 20021624 60625 SRX3357293 SRS2656374 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78076 0.83253 0.11443 0.12223 0.84758 0.84774 0.71769 0.71187 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44084 44084 SRR6250366 SRX3357292 SRS2656375 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S1 GSM2838452   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S1 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838452 GSM2838452: wt p4 S1; Danio rerio; RNA Seq GSM2838452   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S1.R1.fastq.gz wt_p4_S1.R2.fastq.gz fastq fastq 30752288.0 549148.0 GSM2838452 r1 0:24 1:32 A:8244560;C:7083728;G:7062913;T:8335315;N:25772 24 32     8244560 7083728 7062913 8335315 25772 SRX3357292 SRS2656375 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76119 0.82205 0.12638 0.13376 0.8857 0.88532 0.7951 0.7962 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44085 44085 SRR6250365 SRX3357291 SRS2656372 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S13 GSM2838451   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S13 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838451 GSM2838451: wt p4 S13; Danio rerio; RNA Seq GSM2838451   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S13.R1.fastq.gz wt_p4_S13.R2.fastq.gz fastq fastq 85813392.0 1532382.0 GSM2838451 r1 0:24 1:32 A:23602233;C:19100017;G:19492573;T:23547883;N:70686 24 32     23602233 19100017 19492573 23547883 70686 SRX3357291 SRS2656372 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77143 0.82139 0.09157 0.09496 0.86257 0.86273 0.72727 0.72502 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44086 44086 SRR6250364 SRX3357290 SRS2656373 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S12 GSM2838450   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S12 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838450 GSM2838450: wt p4 S12; Danio rerio; RNA Seq GSM2838450   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S12.R1.fastq.gz wt_p4_S12.R2.fastq.gz fastq fastq 18404008.0 328643.0 GSM2838450 r1 0:24 1:32 A:5125310;C:3960294;G:4054209;T:5248856;N:15339 24 32     5125310 3960294 4054209 5248856 15339 SRX3357290 SRS2656373 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76331 0.8125 0.0999 0.1021 0.87028 0.87022 0.3061 0.7522 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44087 44087 SRR6250363 SRX3357289 SRS2656371 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S11 GSM2838449   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S11 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838449 GSM2838449: wt p4 S11; Danio rerio; RNA Seq GSM2838449   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S11.R1.fastq.gz wt_p4_S11.R2.fastq.gz fastq fastq 81838568.0 1461403.0 GSM2838449 r1 0:24 1:32 A:22067792;C:18616034;G:18950203;T:22137237;N:67302 24 32     22067792 18616034 18950203 22137237 67302 SRX3357289 SRS2656371 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77673 0.82676 0.11823 0.12552 0.8619 0.86399 0.73261 0.73128 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44088 44088 SRR6250362 SRX3357288 SRS2656370 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p4 S10 GSM2838448   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB wt p4 S10 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:Wild type TLAB GSM2838448 GSM2838448: wt p4 S10; Danio rerio; RNA Seq GSM2838448   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p4_S10.R1.fastq.gz wt_p4_S10.R2.fastq.gz fastq fastq 77205912.0 1378677.0 GSM2838448 r1 0:24 1:32 A:20905304;C:17521218;G:17939726;T:20777228;N:62436 24 32     20905304 17521218 17939726 20777228 62436 SRX3357288 SRS2656370 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77761 0.83011 0.12382 0.13254 0.86429 0.8647 0.78439 0.78658 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44089 44089 SRR6250361 SRX3357287 SRS2656369 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S9 GSM2838447   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S9 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838447 GSM2838447: wt p3 S9; Danio rerio; RNA Seq GSM2838447   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S9.R1.fastq.gz wt_p3_S9.R2.fastq.gz fastq fastq 2408.0 43.0 GSM2838447 r1 0:24 1:32 A:630;C:591;G:610;T:577;N:0 24 32     630 591 610 577 0 SRX3357287 SRS2656369 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.91429 0.36364 0.2 0.0909 0.99963 0.99995 0.68 0.66666 24 32 B T mate2 technical by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44090 44090 SRR6250360 SRX3357286 SRS2656368 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S8 GSM2838446   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S8 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838446 GSM2838446: wt p3 S8; Danio rerio; RNA Seq GSM2838446   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S8.R1.fastq.gz wt_p3_S8.R2.fastq.gz fastq fastq 1960.0 35.0 GSM2838446 r1 0:24 1:32 A:469;C:513;G:516;T:462;N:0 24 32     469 513 516 462 0 SRX3357286 SRS2656368 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.88 0.25 0.2 0.0 0.99975 0.99995 0.82352 1.0 24 32 B B mate2-mate1 similar by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44091 44091 SRR6250359 SRX3357284 SRS2656366 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S7 GSM2838445   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S7 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838445 GSM2838445: wt p3 S7; Danio rerio; RNA Seq GSM2838445   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S7.R1.fastq.gz wt_p3_S7.R2.fastq.gz fastq fastq 81620280.0 1457505.0 GSM2838445 r1 0:24 1:32 A:21949726;C:18710660;G:19026412;T:21867186;N:66296 24 32     21949726 18710660 19026412 21867186 66296 SRX3357284 SRS2656366 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77869 0.82733 0.14008 0.14886 0.87267 0.8731 0.75824 0.75902 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44092 44092 SRR6250358 SRX3357283 SRS2656365 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S6 GSM2838444   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S6 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838444 GSM2838444: wt p3 S6; Danio rerio; RNA Seq GSM2838444   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S6.R1.fastq.gz wt_p3_S6.R2.fastq.gz fastq fastq 84061488.0 1501098.0 GSM2838444 r1 0:24 1:32 A:22377525;C:19468302;G:19754703;T:22392074;N:68884 24 32     22377525 19468302 19754703 22392074 68884 SRX3357283 SRS2656365 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77689 0.82863 0.14263 0.15362 0.87349 0.87393 0.75351 0.75807 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44093 44093 SRR6250357 SRX3357282 SRS2656364 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S5 GSM2838443   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S5 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838443 GSM2838443: wt p3 S5; Danio rerio; RNA Seq GSM2838443   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S5.R1.fastq.gz wt_p3_S5.R2.fastq.gz fastq fastq 74747288.0 1334773.0 GSM2838443 r1 0:24 1:32 A:20321491;C:16963983;G:17283545;T:20116200;N:62069 24 32     20321491 16963983 17283545 20116200 62069 SRX3357282 SRS2656364 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77498 0.82709 0.10755 0.11552 0.89037 0.89351 0.76636 0.27591 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44094 44094 SRR6250356 SRX3357281 SRS2656363 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S4 GSM2838442   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S4 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838442 GSM2838442: wt p3 S4; Danio rerio; RNA Seq GSM2838442   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S4.R1.fastq.gz wt_p3_S4.R2.fastq.gz fastq fastq 39749248.0 709808.0 GSM2838442 r1 0:24 1:32 A:10051657;C:9639959;G:9805405;T:10220223;N:32004 24 32     10051657 9639959 9805405 10220223 32004 SRX3357281 SRS2656363 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76312 0.82257 0.18031 0.19838 0.91256 0.91441 0.69462 0.6963 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44095 44095 SRR6250355 SRX3357280 SRS2656362 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S3 GSM2838441   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S3 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838441 GSM2838441: wt p3 S3; Danio rerio; RNA Seq GSM2838441   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S3.R1.fastq.gz wt_p3_S3.R2.fastq.gz fastq fastq 82460168.0 1472503.0 GSM2838441 r1 0:24 1:32 A:22042758;C:18983786;G:19250852;T:22115614;N:67158 24 32     22042758 18983786 19250852 22115614 67158 SRX3357280 SRS2656362 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77578 0.82888 0.146 0.15612 0.86036 0.85975 0.72236 0.72759 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44096 44096 SRR6250354 SRX3357279 SRS2656360 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S2 GSM2838440   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S2 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838440 GSM2838440: wt p3 S2; Danio rerio; RNA Seq GSM2838440   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S2.R1.fastq.gz wt_p3_S2.R2.fastq.gz fastq fastq 76462176.0 1365396.0 GSM2838440 r1 0:24 1:32 A:20555351;C:17529474;G:17780648;T:20532935;N:63768 24 32     20555351 17529474 17780648 20532935 63768 SRX3357279 SRS2656360 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77938 0.8309 0.14163 0.15224 0.87026 0.87107 0.75973 0.76003 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44097 44097 SRR6250353 SRX3357278 SRS2656361 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S22 GSM2838439   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S22 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838439 GSM2838439: wt p3 S22; Danio rerio; RNA Seq GSM2838439   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S22.R1.fastq.gz wt_p3_S22.R2.fastq.gz fastq fastq 2036272.0 36362.0 GSM2838439 r1 0:24 1:32 A:534051;C:482377;G:483159;T:535283;N:1402 24 32     534051 482377 483159 535283 1402 SRX3357278 SRS2656361 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.66771 0.73881 0.15713 0.17328 0.96106 0.9598 0.80537 0.79672 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44098 44098 SRR6250352 SRX3357277 SRS2656359 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S21 GSM2838438   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S21 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838438 GSM2838438: wt p3 S21; Danio rerio; RNA Seq GSM2838438   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S21.R1.fastq.gz wt_p3_S21.R2.fastq.gz fastq fastq 70786688.0 1264048.0 GSM2838438 r1 0:24 1:32 A:19153365;C:16090791;G:16426864;T:19057852;N:57816 24 32     19153365 16090791 16426864 19057852 57816 SRX3357277 SRS2656359 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77531 0.82953 0.13952 0.15031 0.89173 0.89232 0.78154 0.7875 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44099 44099 SRR6250351 SRX3357276 SRS2656358 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S20 GSM2838437   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S20 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838437 GSM2838437: wt p3 S20; Danio rerio; RNA Seq GSM2838437   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S20.R1.fastq.gz wt_p3_S20.R2.fastq.gz fastq fastq 62717480.0 1119955.0 GSM2838437 r1 0:24 1:32 A:16708793;C:14490527;G:14735590;T:16732752;N:49818 24 32     16708793 14490527 14735590 16732752 49818 SRX3357276 SRS2656358 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7819 0.82495 0.17803 0.18865 0.86324 0.86302 0.69854 0.69264 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44100 44100 SRR6250350 SRX3357275 SRS2656357 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S1 GSM2838436   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S1 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838436 GSM2838436: wt p3 S1; Danio rerio; RNA Seq GSM2838436   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S1.R1.fastq.gz wt_p3_S1.R2.fastq.gz fastq fastq 61764192.0 1102932.0 GSM2838436 r1 0:24 1:32 A:16403874;C:14300360;G:14565962;T:16444107;N:49889 24 32     16403874 14300360 14565962 16444107 49889 SRX3357275 SRS2656357 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7857 0.83481 0.16212 0.17189 0.85715 0.85642 0.70502 0.71291 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44101 44101 SRR6250349 SRX3357274 SRS2656356 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S19 GSM2838435   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S19 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838435 GSM2838435: wt p3 S19; Danio rerio; RNA Seq GSM2838435   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S19.R1.fastq.gz wt_p3_S19.R2.fastq.gz fastq fastq 60215008.0 1075268.0 GSM2838435 r1 0:24 1:32 A:16139361;C:13746582;G:14054555;T:16224611;N:49899 24 32     16139361 13746582 14054555 16224611 49899 SRX3357274 SRS2656356 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77939 0.83244 0.11193 0.11909 0.88667 0.88824 0.72767 0.71662 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44102 44102 SRR6250348 SRX3357273 SRS2656355 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S18 GSM2838434   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S18 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838434 GSM2838434: wt p3 S18; Danio rerio; RNA Seq GSM2838434   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S18.R1.fastq.gz wt_p3_S18.R2.fastq.gz fastq fastq 86502416.0 1544686.0 GSM2838434 r1 0:24 1:32 A:22690851;C:20247122;G:20556837;T:22936501;N:71105 24 32     22690851 20247122 20556837 22936501 71105 SRX3357273 SRS2656355 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.68812 0.73173 0.16183 0.17229 0.86748 0.8674 0.70363 0.69472 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44103 44103 SRR6250347 SRX3357271 SRS2656353 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S17 GSM2838433   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S17 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838433 GSM2838433: wt p3 S17; Danio rerio; RNA Seq GSM2838433   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S17.R1.fastq.gz wt_p3_S17.R2.fastq.gz fastq fastq 85683024.0 1530054.0 GSM2838433 r1 0:24 1:32 A:22681508;C:19929532;G:20246491;T:22753269;N:72224 24 32     22681508 19929532 20246491 22753269 72224 SRX3357271 SRS2656353 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78043 0.82981 0.16296 0.17534 0.86856 0.86851 0.73198 0.73537 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44104 44104 SRR6250346 SRX3357270 SRS2656354 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S16 GSM2838432   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S16 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838432 GSM2838432: wt p3 S16; Danio rerio; RNA Seq GSM2838432   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S16.R1.fastq.gz wt_p3_S16.R2.fastq.gz fastq fastq 76375544.0 1363849.0 GSM2838432 r1 0:24 1:32 A:19872118;C:18067491;G:18341353;T:20032879;N:61703 24 32     19872118 18067491 18341353 20032879 61703 SRX3357270 SRS2656354 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78228 0.83295 0.18441 0.19896 0.86691 0.86797 0.7169 0.70775 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44105 44105 SRR6250345 SRX3357269 SRS2656351 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S15 GSM2838431   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S15 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838431 GSM2838431: wt p3 S15; Danio rerio; RNA Seq GSM2838431   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S15.R1.fastq.gz wt_p3_S15.R2.fastq.gz fastq fastq 77270816.0 1379836.0 GSM2838431 r1 0:24 1:32 A:20604868;C:17888374;G:18173946;T:20541155;N:62473 24 32     20604868 17888374 18173946 20541155 62473 SRX3357269 SRS2656351 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78034 0.83192 0.15119 0.16258 0.86943 0.87004 0.73186 0.73196 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44106 44106 SRR6250344 SRX3357268 SRS2656350 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S14 GSM2838430   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S14 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838430 GSM2838430: wt p3 S14; Danio rerio; RNA Seq GSM2838430   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S14.R1.fastq.gz wt_p3_S14.R2.fastq.gz fastq fastq 72452464.0 1293794.0 GSM2838430 r1 0:24 1:32 A:19506576;C:16600430;G:16874190;T:19412739;N:58529 24 32     19506576 16600430 16874190 19412739 58529 SRX3357268 SRS2656350 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77447 0.82555 0.13844 0.1491 0.88915 0.88939 0.77862 0.78435 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44107 44107 SRR6250343 SRX3357267 SRS2656349 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S13 GSM2838429   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S13 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838429 GSM2838429: wt p3 S13; Danio rerio; RNA Seq GSM2838429   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S13.R1.fastq.gz wt_p3_S13.R2.fastq.gz fastq fastq 77600880.0 1385730.0 GSM2838429 r1 0:24 1:32 A:20408069;C:18159300;G:18461922;T:20508697;N:62892 24 32     20408069 18159300 18461922 20508697 62892 SRX3357267 SRS2656349 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7812 0.83306 0.18183 0.19603 0.86225 0.86373 0.70873 0.70613 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44108 44108 SRR6250342 SRX3357266 SRS2656348 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S12 GSM2838428   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S12 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838428 GSM2838428: wt p3 S12; Danio rerio; RNA Seq GSM2838428   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S12.R1.fastq.gz wt_p3_S12.R2.fastq.gz fastq fastq 67502568.0 1205403.0 GSM2838428 r1 0:24 1:32 A:18195431;C:15418993;G:15695230;T:18137911;N:55003 24 32     18195431 15418993 15695230 18137911 55003 SRX3357266 SRS2656348 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77379 0.82796 0.13406 0.14349 0.88256 0.88258 0.76096 0.7618 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44109 44109 SRR6250341 SRX3357265 SRS2656347 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S11 GSM2838427   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S11 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838427 GSM2838427: wt p3 S11; Danio rerio; RNA Seq GSM2838427   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S11.R1.fastq.gz wt_p3_S11.R2.fastq.gz fastq fastq 2408.0 43.0 GSM2838427 r1 0:24 1:32 A:568;C:630;G:651;T:559;N:0 24 32     568 630 651 559 0 SRX3357265 SRS2656347 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7742 0.38462 0.35483 0.07692 0.99977 0.99991 0.6923 1.0 24 32 B B mate2-mate1 similar by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44110 44110 SRR6250340 SRX3357264 SRS2656346 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p3 S10 GSM2838426   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB wt p3 S10 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:Wild type TLAB GSM2838426 GSM2838426: wt p3 S10; Danio rerio; RNA Seq GSM2838426   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p3_S10.R1.fastq.gz wt_p3_S10.R2.fastq.gz fastq fastq 1064.0 19.0 GSM2838426 r1 0:24 1:32 A:242;C:270;G:291;T:261;N:0 24 32     242 270 291 261 0 SRX3357264 SRS2656346 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.63637 0.66667 0.0 0.33333 0.99989 0.99997 0.71428 1.0 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44111 44111 SRR6250339 SRX3357263 SRS2656344 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S9 GSM2838425   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S9 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838425 GSM2838425: wt p2 S9; Danio rerio; RNA Seq GSM2838425   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S9.R1.fastq.gz wt_p2_S9.R2.fastq.gz fastq fastq 40783792.0 728282.0 GSM2838425 r1 0:24 1:32 A:10649223;C:9569702;G:9637527;T:10894504;N:32836 24 32     10649223 9569702 9637527 10894504 32836 SRX3357263 SRS2656344 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7906 0.84558 0.20591 0.21966 0.85865 0.85898 0.71966 0.72194 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44112 44112 SRR6250338 SRX3357262 SRS2656343 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S8 GSM2838424   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S8 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838424 GSM2838424: wt p2 S8; Danio rerio; RNA Seq GSM2838424   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S8.R1.fastq.gz wt_p2_S8.R2.fastq.gz fastq fastq 39089400.0 698025.0 GSM2838424 r1                       SRX3357262 SRS2656343 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78394 0.82511 0.20608 0.21878 0.86882 0.86998 0.69976 0.71133 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44113 44113 SRR6250337 SRX3357261 SRS2656342 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S7 GSM2838423   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S7 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838423 GSM2838423: wt p2 S7; Danio rerio; RNA Seq GSM2838423   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S7.R1.fastq.gz wt_p2_S7.R2.fastq.gz fastq fastq 38703896.0 691141.0 GSM2838423 r1 0:24 1:32 A:10311865;C:8903162;G:8992515;T:10465321;N:31033 24 32     10311865 8903162 8992515 10465321 31033 SRX3357261 SRS2656342 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76715 0.8157 0.17322 0.18486 0.865 0.86665 0.6579 0.66292 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44114 44114 SRR6250336 SRX3357260 SRS2656341 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S6 GSM2838422   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S6 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838422 GSM2838422: wt p2 S6; Danio rerio; RNA Seq GSM2838422   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S6.R1.fastq.gz wt_p2_S6.R2.fastq.gz fastq fastq 30542456.0 545401.0 GSM2838422 r1 0:24 1:32 A:8033321;C:7107172;G:7164454;T:8209836;N:27673 24 32     8033321 7107172 7164454 8209836 27673 SRX3357260 SRS2656341 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78373 0.83414 0.18981 0.2014 0.86235 0.86373 0.6968 0.7005 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44115 44115 SRR6250335 SRX3357259 SRS2656340 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S5 GSM2838421   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S5 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838421 GSM2838421: wt p2 S5; Danio rerio; RNA Seq GSM2838421   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S5.R1.fastq.gz wt_p2_S5.R2.fastq.gz fastq fastq 34959568.0 624278.0 GSM2838421 r1 0:24 1:32 A:9180546;C:8129519;G:8220988;T:9399705;N:28810 24 32     9180546 8129519 8220988 9399705 28810 SRX3357259 SRS2656340 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78476 0.83524 0.21505 0.22989 0.86208 0.8636 0.67586 0.67373 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44116 44116 SRR6250334 SRX3357258 SRS2656339 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S4 GSM2838420   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S4 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838420 GSM2838420: wt p2 S4; Danio rerio; RNA Seq GSM2838420   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S4.R1.fastq.gz wt_p2_S4.R2.fastq.gz fastq fastq 11573184.0 206664.0 GSM2838420 r1 0:24 1:32 A:3099219;C:2620762;G:2639101;T:3203925;N:10177 24 32     3099219 2620762 2639101 3203925 10177 SRX3357258 SRS2656339 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.70775 0.76438 0.31372 0.33513 0.91831 0.92048 0.71842 0.71709 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44117 44117 SRR6250333 SRX3357256 SRS2656338 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S3 GSM2838419   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S3 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838419 GSM2838419: wt p2 S3; Danio rerio; RNA Seq GSM2838419   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S3.R1.fastq.gz wt_p2_S3.R2.fastq.gz fastq fastq 37763040.0 674340.0 GSM2838419 r1 0:24 1:32 A:9993306;C:8699070;G:8817530;T:10222682;N:30452 24 32     9993306 8699070 8817530 10222682 30452 SRX3357256 SRS2656338 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7863 0.83568 0.22435 0.23906 0.84331 0.84228 0.35971 0.66377 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44118 44118 SRR6250332 SRX3357255 SRS2656336 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S2 GSM2838418   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S2 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838418 GSM2838418: wt p2 S2; Danio rerio; RNA Seq GSM2838418   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S2.R1.fastq.gz wt_p2_S2.R2.fastq.gz fastq fastq 32485040.0 580090.0 GSM2838418 r1 0:24 1:32 A:8505580;C:7579715;G:7669107;T:8703486;N:27152 24 32     8505580 7579715 7669107 8703486 27152 SRX3357255 SRS2656336 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7719 0.82478 0.20255 0.21629 0.85234 0.85313 0.65578 0.64124 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44119 44119 SRR6250331 SRX3357254 SRS2656334 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S1 GSM2838417   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S1 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838417 GSM2838417: wt p2 S1; Danio rerio; RNA Seq GSM2838417   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S1.R1.fastq.gz wt_p2_S1.R2.fastq.gz fastq fastq 36153488.0 645598.0 GSM2838417 r1 0:24 1:32 A:9482693;C:8433376;G:8529260;T:9678247;N:29912 24 32     9482693 8433376 8529260 9678247 29912 SRX3357254 SRS2656334 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7857 0.83959 0.20506 0.22028 0.85102 0.85121 0.68415 0.69308 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44120 44120 SRR6250330 SRX3357253 SRS2656335 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S14 GSM2838416   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S14 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838416 GSM2838416: wt p2 S14; Danio rerio; RNA Seq GSM2838416   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S14.R1.fastq.gz wt_p2_S14.R2.fastq.gz fastq fastq 35662032.0 636822.0 GSM2838416 r1 0:24 1:32 A:9220957;C:8441374;G:8533782;T:9437149;N:28770 24 32     9220957 8441374 8533782 9437149 28770 SRX3357253 SRS2656335 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78999 0.8417 0.21214 0.22792 0.85397 0.85421 0.68135 0.68129 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44121 44121 SRR6250329 SRX3357252 SRS2656333 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S13 GSM2838415   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S13 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838415 GSM2838415: wt p2 S13; Danio rerio; RNA Seq GSM2838415   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S13.R1.fastq.gz wt_p2_S13.R2.fastq.gz fastq fastq 35179312.0 628202.0 GSM2838415 r1 0:24 1:32 A:9165054;C:8266293;G:8343113;T:9376252;N:28600 24 32     9165054 8266293 8343113 9376252 28600 SRX3357252 SRS2656333 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78329 0.83757 0.22073 0.23652 0.87048 0.87054 0.68987 0.69553 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44122 44122 SRR6250328 SRX3357251 SRS2656331 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S12 GSM2838414   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S12 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838414 GSM2838414: wt p2 S12; Danio rerio; RNA Seq GSM2838414   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S12.R1.fastq.gz wt_p2_S12.R2.fastq.gz fastq fastq 39207392.0 700132.0 GSM2838414 r1 0:24 1:32 A:10192020;C:9230236;G:9318388;T:10435252;N:31496 24 32     10192020 9230236 9318388 10435252 31496 SRX3357251 SRS2656331 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78483 0.84016 0.22133 0.23855 0.8743 0.8757 0.70284 0.70386 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44123 44123 SRR6250327 SRX3357250 SRS2656332 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S11 GSM2838413   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S11 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838413 GSM2838413: wt p2 S11; Danio rerio; RNA Seq GSM2838413   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S11.R1.fastq.gz wt_p2_S11.R2.fastq.gz fastq fastq 40102944.0 716124.0 GSM2838413 r1 0:24 1:32 A:10511641;C:9360932;G:9463806;T:10731533;N:35032 24 32     10511641 9360932 9463806 10731533 35032 SRX3357250 SRS2656332 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78698 0.83686 0.21254 0.22573 0.85985 0.86011 0.67858 0.67878 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44124 44124 SRR6250326 SRX3357249 SRS2656330 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p2 S10 GSM2838412   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB wt p2 S10 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p2|genotype:Wild type TLAB GSM2838412 GSM2838412: wt p2 S10; Danio rerio; RNA Seq GSM2838412   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p2_S10.R1.fastq.gz wt_p2_S10.R2.fastq.gz fastq fastq 44972536.0 803081.0 GSM2838412 r1 0:24 1:32 A:11615173;C:10671699;G:10744448;T:11903998;N:37218 24 32     11615173 10671699 10744448 11903998 37218 SRX3357249 SRS2656330 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78871 0.84338 0.21928 0.23653 0.8574 0.85772 0.71222 0.69441 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44125 44125 SRR6250325 SRX3357248 SRS2656329 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p1 S3 GSM2838411   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB wt p1 S3 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB GSM2838411 GSM2838411: wt p1 S3; Danio rerio; RNA Seq GSM2838411   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p1_S3.R1.fastq.gz wt_p1_S3.R2.fastq.gz fastq fastq 95933432.0 1713097.0 GSM2838411 r1 0:24 1:32 A:26332108;C:21430855;G:21729899;T:26360908;N:79662 24 32     26332108 21430855 21729899 26360908 79662 SRX3357248 SRS2656329 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78047 0.82824 0.10747 0.11108 0.86304 0.86352 0.73589 0.73908 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44126 44126 SRR6250324 SRX3357247 SRS2656328 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p1 S2 GSM2838410   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB wt p1 S2 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB GSM2838410 GSM2838410: wt p1 S2; Danio rerio; RNA Seq GSM2838410   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p1_S2.R1.fastq.gz wt_p1_S2.R2.fastq.gz fastq fastq 88254208.0 1575968.0 GSM2838410 r1 0:24 1:32 A:24065563;C:19830888;G:20138155;T:24147163;N:72439 24 32     24065563 19830888 20138155 24147163 72439 SRX3357247 SRS2656328 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76816 0.81423 0.11267 0.11725 0.83956 0.83913 0.72098 0.72128 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44127 44127 SRR6250323 SRX3357246 SRS2656327 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   wt p1 S1 GSM2838409   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB wt p1 S1 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p1|genotype:Wild type TLAB GSM2838409 GSM2838409: wt p1 S1; Danio rerio; RNA Seq GSM2838409   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     wt_p1_S1.R1.fastq.gz wt_p1_S1.R2.fastq.gz fastq fastq 69214768.0 1235978.0 GSM2838409 r1 0:24 1:32 A:19113770;C:15404084;G:15514812;T:19124524;N:57578 24 32     19113770 15404084 15514812 19124524 57578 SRX3357246 SRS2656327 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78022 0.83006 0.09266 0.09517 0.87032 0.87056 0.74712 0.74427 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44128 44128 SRR6250322 SRX3357245 SRS2656326 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S9 GSM2838408   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S9 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838408 GSM2838408: oep p4 S9; Danio rerio; RNA Seq GSM2838408   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S9.R1.fastq.gz oep_p4_S9.R2.fastq.gz fastq fastq 59607240.0 1064415.0 GSM2838408 r1 0:24 1:32 A:15889806;C:13717017;G:13980126;T:15971426;N:48865 24 32     15889806 13717017 13980126 15971426 48865 SRX3357245 SRS2656326 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.70468 0.74568 0.12923 0.13658 0.87969 0.87998 0.75196 0.7565 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44129 44129 SRR6250321 SRX3357244 SRS2656325 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S8 GSM2838407   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S8 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838407 GSM2838407: oep p4 S8; Danio rerio; RNA Seq GSM2838407   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S8.R1.fastq.gz oep_p4_S8.R2.fastq.gz fastq fastq 90621608.0 1618243.0 GSM2838407 r1 0:24 1:32 A:23755286;C:21263521;G:21526665;T:23999805;N:76331 24 32     23755286 21263521 21526665 23999805 76331 SRX3357244 SRS2656325 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80318 0.85365 0.18029 0.19282 0.85283 0.85271 0.70396 0.69979 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44130 44130 SRR6250320 SRX3357243 SRS2656324 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S7 GSM2838406   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S7 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838406 GSM2838406: oep p4 S7; Danio rerio; RNA Seq GSM2838406   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S7.R1.fastq.gz oep_p4_S7.R2.fastq.gz fastq fastq 4912656.0 87726.0 GSM2838406 r1 0:24 1:32 A:1332044;C:1105801;G:1114366;T:1356143;N:4302 24 32     1332044 1105801 1114366 1356143 4302 SRX3357243 SRS2656324 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79097 0.83957 0.1723 0.18179 0.89852 0.89674 0.75439 0.74413 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44131 44131 SRR6250319 SRX3357241 SRS2656323 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S6 GSM2838405   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S6 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838405 GSM2838405: oep p4 S6; Danio rerio; RNA Seq GSM2838405   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S6.R1.fastq.gz oep_p4_S6.R2.fastq.gz fastq fastq 93200072.0 1664287.0 GSM2838405 r1 0:24 1:32 A:25640963;C:20843604;G:21078374;T:25559248;N:77883 24 32     25640963 20843604 21078374 25559248 77883 SRX3357241 SRS2656323 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80049 0.84734 0.10078 0.10503 0.88921 0.89045 0.76168 0.75227 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44132 44132 SRR6250318 SRX3357240 SRS2656321 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S5 GSM2838404   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S5 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838404 GSM2838404: oep p4 S5; Danio rerio; RNA Seq GSM2838404   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S5.R1.fastq.gz oep_p4_S5.R2.fastq.gz fastq fastq 98958440.0 1767115.0 GSM2838404 r1 0:24 1:32 A:26086584;C:23066643;G:23403459;T:26320507;N:81247 24 32     26086584 23066643 23403459 26320507 81247 SRX3357240 SRS2656321 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79971 0.85115 0.18891 0.20331 0.85896 0.85995 0.71987 0.71776 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44133 44133 SRR6250317 SRX3357239 SRS2656319 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S4 GSM2838403   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S4 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838403 GSM2838403: oep p4 S4; Danio rerio; RNA Seq GSM2838403   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S4.R1.fastq.gz oep_p4_S4.R2.fastq.gz fastq fastq 100896152.0 1801717.0 GSM2838403 r1 0:24 1:32 A:27173990;C:23092381;G:23338548;T:27207074;N:84159 24 32     27173990 23092381 23338548 27207074 84159 SRX3357239 SRS2656319 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80448 0.85347 0.12574 0.13447 0.86975 0.87125 0.76815 0.76891 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44134 44134 SRR6250316 SRX3357238 SRS2656320 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S3 GSM2838402   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S3 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838402 GSM2838402: oep p4 S3; Danio rerio; RNA Seq GSM2838402   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S3.R1.fastq.gz oep_p4_S3.R2.fastq.gz fastq fastq 12183136.0 217556.0 GSM2838402 r1 0:24 1:32 A:3345072;C:2686784;G:2709001;T:3432792;N:9487 24 32     3345072 2686784 2709001 3432792 9487 SRX3357238 SRS2656320 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79372 0.84371 0.14527 0.15384 0.87071 0.86916 0.76333 0.76589 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44135 44135 SRR6250315 SRX3357237 SRS2656318 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S2 GSM2838401   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S2 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838401 GSM2838401: oep p4 S2; Danio rerio; RNA Seq GSM2838401   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S2.R1.fastq.gz oep_p4_S2.R2.fastq.gz fastq fastq 107148720.0 1913370.0 GSM2838401 r1 0:24 1:32 A:28268122;C:25019759;G:25347800;T:28424142;N:88897 24 32     28268122 25019759 25347800 28424142 88897 SRX3357237 SRS2656318 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.8032 0.85403 0.16972 0.18136 0.8548 0.85409 0.72899 0.72574 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44136 44136 SRR6250314 SRX3357236 SRS2656399 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S27 GSM2838400   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S27 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838400 GSM2838400: oep p4 S27; Danio rerio; RNA Seq GSM2838400   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S27.R1.fastq.gz oep_p4_S27.R2.fastq.gz fastq fastq 2688.0 48.0 GSM2838400 r1 0:24 1:32 A:651;C:681;G:654;T:671;N:31 24 32     651 681 654 671 31 SRX3357236 SRS2656399 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.69231 0.72728 0.15384 0.36363 0.99965 0.99991 0.80952 0.75 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44137 44137 SRR6250313 SRX3357235 SRS2656317 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S26 GSM2838399   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S26 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838399 GSM2838399: oep p4 S26; Danio rerio; RNA Seq GSM2838399   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S26.R1.fastq.gz oep_p4_S26.R2.fastq.gz fastq fastq 22568.0 403.0 GSM2838399 r1 0:24 1:32 A:6226;C:6218;G:5042;T:5082;N:0 24 32     6226 6218 5042 5082 0 SRX3357235 SRS2656317 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.10363 0.21244 0.06994 0.13989 0.99979 0.99977 0.83333 0.84615 24 32 B B mate1-mate2 similar by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44138 44138 SRR6250312 SRX3357234 SRS2656316 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S25 GSM2838398   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S25 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838398 GSM2838398: oep p4 S25; Danio rerio; RNA Seq GSM2838398   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S25.R1.fastq.gz oep_p4_S25.R2.fastq.gz fastq fastq 54054560.0 965260.0 GSM2838398 r1 0:24 1:32 A:15083196;C:11824083;G:12012704;T:15089704;N:44873 24 32     15083196 11824083 12012704 15089704 44873 SRX3357234 SRS2656316 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77823 0.82959 0.09938 0.10266 0.87247 0.87261 0.75693 0.75981 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44139 44139 SRR6250311 SRX3357233 SRS2656315 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S24 GSM2838397   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S24 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838397 GSM2838397: oep p4 S24; Danio rerio; RNA Seq GSM2838397   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S24.R1.fastq.gz oep_p4_S24.R2.fastq.gz fastq fastq 65370312.0 1167327.0 GSM2838397 r1 0:24 1:32 A:18166371;C:14411204;G:14686361;T:18054122;N:52254 24 32     18166371 14411204 14686361 18054122 52254 SRX3357233 SRS2656315 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77848 0.8339 0.06212 0.06417 0.88286 0.88258 0.77544 0.77309 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44140 44140 SRR6250310 SRX3357232 SRS2656314 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S23 GSM2838396   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S23 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838396 GSM2838396: oep p4 S23; Danio rerio; RNA Seq GSM2838396   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S23.R1.fastq.gz oep_p4_S23.R2.fastq.gz fastq fastq 70100016.0 1251786.0 GSM2838396 r1 0:24 1:32 A:19312414;C:15561812;G:15849161;T:19318033;N:58596 24 32     19312414 15561812 15849161 19318033 58596 SRX3357232 SRS2656314 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7756 0.82639 0.09516 0.09729 0.85009 0.85107 0.70903 0.71057 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44141 44141 SRR6250309 SRX3357231 SRS2656312 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S22 GSM2838395   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S22 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838395 GSM2838395: oep p4 S22; Danio rerio; RNA Seq GSM2838395   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S22.R1.fastq.gz oep_p4_S22.R2.fastq.gz fastq fastq 4747120.0 84770.0 GSM2838395 r1 0:24 1:32 A:1288548;C:1060321;G:1081126;T:1313197;N:3928 24 32     1288548 1060321 1081126 1313197 3928 SRX3357231 SRS2656312 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76295 0.81806 0.13024 0.13447 0.90376 0.90264 0.73271 0.73327 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44142 44142 SRR6250308 SRX3357230 SRS2656313 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S21 GSM2838394   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S21 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838394 GSM2838394: oep p4 S21; Danio rerio; RNA Seq GSM2838394   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S21.R1.fastq.gz oep_p4_S21.R2.fastq.gz fastq fastq 69224624.0 1236154.0 GSM2838394 r1 0:24 1:32 A:19150005;C:15344900;G:15612847;T:19059784;N:57088 24 32     19150005 15344900 15612847 19059784 57088 SRX3357230 SRS2656313 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78186 0.83463 0.08972 0.09272 0.86523 0.8648 0.76414 0.7627 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44143 44143 SRR6250307 SRX3357229 SRS2656311 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S20 GSM2838393   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S20 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838393 GSM2838393: oep p4 S20; Danio rerio; RNA Seq GSM2838393   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S20.R1.fastq.gz oep_p4_S20.R2.fastq.gz fastq fastq 63875952.0 1140642.0 GSM2838393 r1 0:24 1:32 A:17811278;C:14030742;G:14262763;T:17718107;N:53062 24 32     17811278 14030742 14262763 17718107 53062 SRX3357229 SRS2656311 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.782 0.83525 0.06874 0.07014 0.86618 0.86671 0.77992 0.78773 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44144 44144 SRR6250306 SRX3357228 SRS2656310 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S1 GSM2838392   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S1 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838392 GSM2838392: oep p4 S1; Danio rerio; RNA Seq GSM2838392   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S1.R1.fastq.gz oep_p4_S1.R2.fastq.gz fastq fastq 101140480.0 1806080.0 GSM2838392 r1 0:24 1:32 A:26745478;C:23576874;G:23869258;T:26866139;N:82731 24 32     26745478 23576874 23869258 26866139 82731 SRX3357228 SRS2656310 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80153 0.85401 0.14352 0.15536 0.85957 0.86048 0.7519 0.75548 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44145 44145 SRR6250305 SRX3357227 SRS2656309 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S19 GSM2838391   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S19 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838391 GSM2838391: oep p4 S19; Danio rerio; RNA Seq GSM2838391   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S19.R1.fastq.gz oep_p4_S19.R2.fastq.gz fastq fastq 69556088.0 1242073.0 GSM2838391 r1 0:24 1:32 A:19403027;C:15217162;G:15475096;T:19405287;N:55516 24 32     19403027 15217162 15475096 19405287 55516 SRX3357227 SRS2656309 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76838 0.81461 0.07623 0.07663 0.85788 0.85811 0.73855 0.7503 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44146 44146 SRR6250304 SRX3357226 SRS2656308 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S18 GSM2838390   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S18 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838390 GSM2838390: oep p4 S18; Danio rerio; RNA Seq GSM2838390   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S18.R1.fastq.gz oep_p4_S18.R2.fastq.gz fastq fastq 4183704.0 74709.0 GSM2838390 r1                       SRX3357226 SRS2656308 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77453 0.81404 0.07859 0.08027 0.90053 0.90011 0.77064 0.30009 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44147 44147 SRR6250303 SRX3357225 SRS2656307 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S17 GSM2838389   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S17 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838389 GSM2838389: oep p4 S17; Danio rerio; RNA Seq GSM2838389   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S17.R1.fastq.gz oep_p4_S17.R2.fastq.gz fastq fastq 92090936.0 1644481.0 GSM2838389 r1 0:24 1:32 A:25372860;C:20478356;G:20907685;T:25257246;N:74789 24 32     25372860 20478356 20907685 25257246 74789 SRX3357225 SRS2656307 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78048 0.83088 0.06347 0.06502 0.84926 0.84916 0.73295 0.73519 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44148 44148 SRR6250302 SRX3357224 SRS2656306 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S16 GSM2838388   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S16 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838388 GSM2838388: oep p4 S16; Danio rerio; RNA Seq GSM2838388   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S16.R1.fastq.gz oep_p4_S16.R2.fastq.gz fastq fastq 78362088.0 1399323.0 GSM2838388 r1 0:24 1:32 A:21627730;C:17366835;G:17737716;T:21567579;N:62228 24 32     21627730 17366835 17737716 21567579 62228 SRX3357224 SRS2656306 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.76846 0.81735 0.0843 0.08632 0.85851 0.85847 0.74942 0.75016 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44149 44149 SRR6250301 SRX3357223 SRS2656305 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S15 GSM2838387   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S15 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838387 GSM2838387: oep p4 S15; Danio rerio; RNA Seq GSM2838387   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S15.R1.fastq.gz oep_p4_S15.R2.fastq.gz fastq fastq 3443832.0 61497.0 GSM2838387 r1 0:24 1:32 A:899084;C:804618;G:810086;T:927528;N:2516 24 32     899084 804618 810086 927528 2516 SRX3357223 SRS2656305 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.77278 0.83379 0.18796 0.2009 0.90871 0.90514 0.34291 0.71589 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44150 44150 SRR6250300 SRX3357222 SRS2656304 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S14 GSM2838386   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S14 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838386 GSM2838386: oep p4 S14; Danio rerio; RNA Seq GSM2838386   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S14.R1.fastq.gz oep_p4_S14.R2.fastq.gz fastq fastq 84153440.0 1502740.0 GSM2838386 r1 0:24 1:32 A:22314812;C:19454797;G:19684266;T:22631594;N:67971 24 32     22314812 19454797 19684266 22631594 67971 SRX3357222 SRS2656304 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78868 0.84021 0.15916 0.17058 0.84327 0.8434 0.71882 0.72779 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44151 44151 SRR6250299 SRX3357221 SRS2656303 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S13 GSM2838385   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S13 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838385 GSM2838385: oep p4 S13; Danio rerio; RNA Seq GSM2838385   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S13.R1.fastq.gz oep_p4_S13.R2.fastq.gz fastq fastq 65871120.0 1176270.0 GSM2838385 r1 0:24 1:32 A:17192209;C:15459137;G:15653476;T:17512736;N:53562 24 32     17192209 15459137 15653476 17512736 53562 SRX3357221 SRS2656303 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78914 0.84191 0.19002 0.20308 0.84088 0.83968 0.67593 0.67633 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44152 44152 SRR6250298 SRX3357220 SRS2656302 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S12 GSM2838384   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S12 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838384 GSM2838384: oep p4 S12; Danio rerio; RNA Seq GSM2838384   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S12.R1.fastq.gz oep_p4_S12.R2.fastq.gz fastq fastq 75987520.0 1356920.0 GSM2838384 r1 0:24 1:32 A:20433443;C:17367926;G:17661569;T:20460743;N:63839 24 32     20433443 17367926 17661569 20460743 63839 SRX3357220 SRS2656302 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78514 0.83059 0.14453 0.15378 0.87091 0.87081 0.72523 0.72866 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44153 44153 SRR6250297 SRX3357219 SRS2656301 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S11 GSM2838383   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S11 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838383 GSM2838383: oep p4 S11; Danio rerio; RNA Seq GSM2838383   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S11.R1.fastq.gz oep_p4_S11.R2.fastq.gz fastq fastq 3793384.0 67739.0 GSM2838383 r1 0:24 1:32 A:1003375;C:874215;G:890420;T:1022315;N:3059 24 32     1003375 874215 890420 1022315 3059 SRX3357219 SRS2656301 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.50843 0.53703 0.11615 0.12129 0.92685 0.926 0.75144 0.74516 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44154 44154 SRR6250296 SRX3357218 SRS2656300 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p4 S10 GSM2838382   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 oep p4 S10 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p4|genotype:MZoep tz57 GSM2838382 GSM2838382: oep p4 S10; Danio rerio; RNA Seq GSM2838382   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p4_S10.R1.fastq.gz oep_p4_S10.R2.fastq.gz fastq fastq 67491256.0 1205201.0 GSM2838382 r1 0:24 1:32 A:18217694;C:15400421;G:15669743;T:18150401;N:52997 24 32     18217694 15400421 15669743 18150401 52997 SRX3357218 SRS2656300 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7981 0.84281 0.13672 0.14575 0.87411 0.87334 0.76971 0.77541 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44155 44155 SRR6250295 SRX3357217 SRS2656299 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S9 GSM2838381   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S9 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838381 GSM2838381: oep p3 S9; Danio rerio; RNA Seq GSM2838381   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S9.R1.fastq.gz oep_p3_S9.R2.fastq.gz fastq fastq 66837680.0 1193530.0 GSM2838381 r1 0:24 1:32 A:17920696;C:15328550;G:15593377;T:17941985;N:53072 24 32     17920696 15328550 15593377 17941985 53072 SRX3357217 SRS2656299 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80301 0.85076 0.13595 0.14553 0.85876 0.8578 0.70612 0.70991 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44156 44156 SRR6250294 SRX3357216 SRS2656297 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S8 GSM2838380   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S8 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838380 GSM2838380: oep p3 S8; Danio rerio; RNA Seq GSM2838380   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S8.R1.fastq.gz oep_p3_S8.R2.fastq.gz fastq fastq 83751080.0 1495555.0 GSM2838380 r1 0:24 1:32 A:22095926;C:19582224;G:19786171;T:22219235;N:67524 24 32     22095926 19582224 19786171 22219235 67524 SRX3357216 SRS2656297 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.8005 0.85154 0.1633 0.17653 0.84461 0.84465 0.74525 0.74414 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44157 44157 SRR6250293 SRX3357215 SRS2656298 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S7 GSM2838379   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S7 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838379 GSM2838379: oep p3 S7; Danio rerio; RNA Seq GSM2838379   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S7.R1.fastq.gz oep_p3_S7.R2.fastq.gz fastq fastq 74253536.0 1325956.0 GSM2838379 r1 0:24 1:32 A:19569753;C:17295764;G:17554585;T:19773058;N:60376 24 32     19569753 17295764 17554585 19773058 60376 SRX3357215 SRS2656298 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79969 0.85144 0.16576 0.17848 0.85003 0.84873 0.72639 0.72085 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44158 44158 SRR6250292 SRX3357214 SRS2656296 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S74 GSM2838378   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S74 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838378 GSM2838378: oep p3 S74; Danio rerio; RNA Seq GSM2838378   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S74.R1.fastq.gz oep_p3_S74.R2.fastq.gz fastq fastq 59001376.0 1053596.0 GSM2838378 r1 0:24 1:32 A:15341220;C:13918217;G:14205278;T:15489081;N:47580 24 32     15341220 13918217 14205278 15489081 47580 SRX3357214 SRS2656296 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78652 0.8396 0.16905 0.18338 0.86151 0.86145 0.72891 0.73043 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44159 44159 SRR6250291 SRX3357213 SRS2656295 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S73 GSM2838377   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S73 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838377 GSM2838377: oep p3 S73; Danio rerio; RNA Seq GSM2838377   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S73.R1.fastq.gz oep_p3_S73.R2.fastq.gz fastq fastq 69861456.0 1247526.0 GSM2838377 r1 0:24 1:32 A:17763729;C:16822790;G:17127718;T:18091717;N:55502 24 32     17763729 16822790 17127718 18091717 55502 SRX3357213 SRS2656295 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.78514 0.84006 0.19824 0.21258 0.84709 0.84571 0.66962 0.67035 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44160 44160 SRR6250290 SRX3357212 SRS2656294 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S72 GSM2838376   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S72 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838376 GSM2838376: oep p3 S72; Danio rerio; RNA Seq GSM2838376   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S72.R1.fastq.gz oep_p3_S72.R2.fastq.gz fastq fastq 76297816.0 1362461.0 GSM2838376 r1 0:24 1:32 A:19487447;C:18321600;G:18646618;T:19779503;N:62648 24 32     19487447 18321600 18646618 19779503 62648 SRX3357212 SRS2656294 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79547 0.85005 0.18506 0.20204 0.83966 0.84011 0.6719 0.67451 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44161 44161 SRR6250289 SRX3357211 SRS2656293 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S71 GSM2838375   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S71 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838375 GSM2838375: oep p3 S71; Danio rerio; RNA Seq GSM2838375   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S71.R1.fastq.gz oep_p3_S71.R2.fastq.gz fastq fastq 75927544.0 1355849.0 GSM2838375 r1 0:24 1:32 A:20268836;C:17477159;G:17830475;T:20289895;N:61179 24 32     20268836 17477159 17830475 20289895 61179 SRX3357211 SRS2656293 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.7933 0.84253 0.14163 0.15232 0.86342 0.86405 0.68068 0.68035 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44162 44162 SRR6250288 SRX3357210 SRS2656292 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S70 GSM2838374   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S70 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838374 GSM2838374: oep p3 S70; Danio rerio; RNA Seq GSM2838374   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S70.R1.fastq.gz oep_p3_S70.R2.fastq.gz fastq fastq 84525840.0 1509390.0 GSM2838374 r1 0:24 1:32 A:22708087;C:19303312;G:19687748;T:22760729;N:65964 24 32     22708087 19303312 19687748 22760729 65964 SRX3357210 SRS2656292 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79226 0.84226 0.14243 0.15278 0.85297 0.85342 0.69822 0.70056 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44163 44163 SRR6250287 SRX3357209 SRS2656291 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S6 GSM2838373   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S6 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838373 GSM2838373: oep p3 S6; Danio rerio; RNA Seq GSM2838373   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S6.R1.fastq.gz oep_p3_S6.R2.fastq.gz fastq fastq 64042216.0 1143611.0 GSM2838373 r1 0:24 1:32 A:17477673;C:14427234;G:14658115;T:17428140;N:51054 24 32     17477673 14427234 14658115 17428140 51054 SRX3357209 SRS2656291 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.80076 0.84841 0.12096 0.12822 0.85318 0.85334 0.7865 0.78575 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44164 44164 SRR6250286 SRX3357208 SRS2656290 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S69 GSM2838372   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S69 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838372 GSM2838372: oep p3 S69; Danio rerio; RNA Seq GSM2838372   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S69.R1.fastq.gz oep_p3_S69.R2.fastq.gz fastq fastq 6585488.0 117598.0 GSM2838372 r1 0:24 1:32 A:1730253;C:1555031;G:1562489;T:1731898;N:5817 24 32     1730253 1555031 1562489 1731898 5817 SRX3357208 SRS2656290 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.75286 0.82078 0.15462 0.17297 0.91445 0.9139 0.77583 0.77999 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44165 44165 SRR6250285 SRX3357207 SRS2656289 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S68 GSM2838371   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S68 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838371 GSM2838371: oep p3 S68; Danio rerio; RNA Seq GSM2838371   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S68.R1.fastq.gz oep_p3_S68.R2.fastq.gz fastq fastq 51989560.0 928385.0 GSM2838371 r1 0:24 1:32 A:13525099;C:12235022;G:12510508;T:13677564;N:41367 24 32     13525099 12235022 12510508 13677564 41367 SRX3357207 SRS2656289 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79086 0.84275 0.1571 0.16871 0.88185 0.88252 0.67648 0.67296 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44166 44166 SRR6250284 SRX3357206 SRS2656288 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S67 GSM2838370   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S67 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838370 GSM2838370: oep p3 S67; Danio rerio; RNA Seq GSM2838370   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S67.R1.fastq.gz oep_p3_S67.R2.fastq.gz fastq fastq 84747488.0 1513348.0 GSM2838370 r1 0:24 1:32 A:22025430;C:20007980;G:20351968;T:22292024;N:70086 24 32     22025430 20007980 20351968 22292024 70086 SRX3357206 SRS2656288 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79678 0.84797 0.17303 0.1864 0.85551 0.85525 0.6823 0.67888 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44167 44167 SRR6250283 SRX3357205 SRS2656287 SRP123526 PRJNA416939 Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage GSE106466 Transcriptome Analysis SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2. parent bioproject:PRJNA417291 pubmed:29700225   oep p3 S66 GSM2838369   tissue:Embryonic cell|developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 oep p3 S66 Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of … Embryonic cell   50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts. Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage. developmental stage:50% epiboly|library preparation batch:p3|genotype:MZoep tz57 GSM2838369 GSM2838369: oep p3 S66; Danio rerio; RNA Seq GSM2838369   1 50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP123526     oep_p3_S66.R1.fastq.gz oep_p3_S66.R2.fastq.gz fastq fastq 74525864.0 1330819.0 GSM2838369 r1 0:24 1:32 A:19200379;C:17757638;G:18093711;T:19414533;N:59603 24 32     19200379 17757638 18093711 19414533 59603 SRX3357205 SRS2656287 SRA627905 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 2 0.79564 0.84753 0.18356 0.1978 0.85614 0.85518 0.68007 0.67596 24 32 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures

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