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22 rows where devstage_curation = "Pharyngula" and tissue_curation_coarse = "Embryo Imprecise"

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experiment.library_selection 3

technology 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Embryo Imprecise · 22 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 22 ✖
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
39623 39623 SRR1914393 SRX955773 SRS873564 SRP056136 PRJNA278119 RNA seq of control and foxo3b MO zebrafish cells. GSE66860 Transcriptome Analysis Gata1+ cells isolated from control and foxo3b MO zebrafish at 24 and 48hpf were subjected to RNA seq and related analyses. Overall design: Gata1 GFP zebrafish stran was utilized embryos were injected with foxo3b MO and standard MO at one cell stage. Gata1+ cells were selected by FACS at 24 and 48hpf and submitted to RNA seq and related analyses.   pubmed:25843800   foxo3b MO 24hpf GSM1633401   tissue:Gata1+ cells|time:24 hpf morpholinos|zebrafish strain:gata1:GFP foxo3b MO 24hpf TopHat for mapping of Hiseq 2000 RNA Seq data Cufflinks for assembling transcripts estimating their abundances and testing for differential expression and regulation in RNA Seq samples Computation and visualization were achieved using the heatmap plus package in R. IPA and the Gene Ontology for functional analysis of specific genes Genome build: Zv9 Gata1+ cells   RNA was extracted by TRIzol Regent. RNA libraries were prepared for sequencing using standard Illumina protocols   time:24 hpf morpholinos|zebrafish strain:gata1:GFP GSM1633401 GSM1633401: foxo3b MO 24hpf; Danio rerio; RNA Seq GSM1633401   1 RNA was extracted by TRIzol Regent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1633401 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP056136     FM24_2.fastq FM24_1.fastq fastq fastq 4602444154.0 22784377.0 GSM1633401 r1 0:101 1:101 A:1213502185;C:1099543456;G:1084624444;T:1201260820;N:3513249 101 101     1213502185 1099543456 1084624444 1201260820 3513249 SRX955773 SRS873564 SRA246560 GEO Beijing Institute of Genomics 2 0.94581 0.94397 0.0658 0.06679 0.69059 0.6952 0.46857 0.4681 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2015-03-13 Pharyngula Embryo Undetermined Embryo Imprecise
39624 39624 SRR1914392 SRX955772 SRS873567 SRP056136 PRJNA278119 RNA seq of control and foxo3b MO zebrafish cells. GSE66860 Transcriptome Analysis Gata1+ cells isolated from control and foxo3b MO zebrafish at 24 and 48hpf were subjected to RNA seq and related analyses. Overall design: Gata1 GFP zebrafish stran was utilized embryos were injected with foxo3b MO and standard MO at one cell stage. Gata1+ cells were selected by FACS at 24 and 48hpf and submitted to RNA seq and related analyses.   pubmed:25843800   Control 24hpf GSM1633400   tissue:Gata1+ cells|time:24 hpf strain:gata1:GFP Control 24hpf TopHat for mapping of Hiseq 2000 RNA Seq data Cufflinks for assembling transcripts estimating their abundances and testing for differential expression and regulation in RNA Seq samples Computation and visualization were achieved using the heatmap plus package in R. IPA and the Gene Ontology for functional analysis of specific genes Genome build: Zv9 Gata1+ cells   RNA was extracted by TRIzol Regent. RNA libraries were prepared for sequencing using standard Illumina protocols   time:24 hpf strain:gata1:GFP GSM1633400 GSM1633400: Control 24hpf; Danio rerio; RNA Seq GSM1633400   1 RNA was extracted by TRIzol Regent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1633400 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP056136     C24_1.fastq C24_2.fastq fastq fastq 8430236690.0 41733845.0 GSM1633400 r1 0:101 1:101 A:2208388816;C:2027781108;G:2005141471;T:2182738518;N:6186777 101 101     2208388816 2027781108 2005141471 2182738518 6186777 SRX955772 SRS873567 SRA246560 GEO Beijing Institute of Genomics 2 0.96552 0.95861 0.05329 0.05466 0.70532 0.71224 0.47594 0.47736 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2015-03-13 Pharyngula Embryo Undetermined Embryo Imprecise
41886 41886 SRR5320523 SRX2619928 SRS2029891 SRP101558 PRJNA378498 Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development GSE95812 Transcriptome Analysis Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.   pubmed:28705894   WT sox10 3 GSM2526402   tissue:Mixed/Ear|developmental stage:36 hpf|genotype:WT|treatment:N1 WT sox10 3 Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample Mixed/Ear   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   developmental stage:36 hpf|genotype:WT|treatment:N1 GSM2526402 GSM2526402: WT sox10 3; Danio rerio; RNA Seq GSM2526402   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM2526402 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP101558     GC-93_L000_R1_001.fastq.gz GC-93_L000_R2_001.fastq.gz fastq fastq 5695089640.0 37467695.0 GSM2526402 r1 0:76 1:76 A:1585564204;C:1219755312;G:1255237513;T:1630829388;N:3703223 76 76     1585564204 1219755312 1255237513 1630829388 3703223 SRX2619928 SRS2029891 SRA543392 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.95516 0.94793 0.11626 0.11413 0.7152 0.73214 0.49379 0.49513 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   United States 2017-03-08 Pharyngula Embryo Undetermined Embryo Imprecise
41887 41887 SRR5320522 SRX2619927 SRS2029890 SRP101558 PRJNA378498 Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development GSE95812 Transcriptome Analysis Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.   pubmed:28705894   WT sox10 2 GSM2526401   tissue:Mixed/Ear|developmental stage:28 hpf|genotype:WT|treatment:N1 WT sox10 2 Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample Mixed/Ear   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   developmental stage:28 hpf|genotype:WT|treatment:N1 GSM2526401 GSM2526401: WT sox10 2; Danio rerio; RNA Seq GSM2526401   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM2526401 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP101558     GC-803_L000_R1_001.fastq.gz GC-803_L000_R2_001_trimmed.fastq.gz fastq fastq 5791936582.0 38320040.0 GSM2526401 r1 0:76 1:75.24 A:1639110583;C:1232145175;G:1255032766;T:1664108558;N:1539500 76 75     1639110583 1232145175 1255032766 1664108558 1539500 SRX2619927 SRS2029890 SRA543392 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.95458 0.94414 0.11651 0.11366 0.72736 0.74337 0.51244 0.48709 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   United States 2017-03-08 Pharyngula Embryo Undetermined Embryo Imprecise
41889 41889 SRR5320520 SRX2619925 SRS2029888 SRP101558 PRJNA378498 Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development GSE95812 Transcriptome Analysis Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.   pubmed:28705894   WT fli1a 3 GSM2526399   tissue:Mixed/Vaculature|developmental stage:36 hpf|genotype:WT|treatment:N1 WT fli1a 3 Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample Mixed/Vaculature   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   developmental stage:36 hpf|genotype:WT|treatment:N1 GSM2526399 GSM2526399: WT fli1a 3; Danio rerio; RNA Seq GSM2526399   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM2526399 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP101558     GC-92_L000_R1_001.fastq.gz GC-92_L000_R2_001.fastq.gz fastq fastq 5947582616.0 39128833.0 GSM2526399 r1 0:76 1:76 A:1646408009;C:1282515077;G:1316726916;T:1698021773;N:3910841 76 76     1646408009 1282515077 1316726916 1698021773 3910841 SRX2619925 SRS2029888 SRA543392 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.94725 0.93969 0.11369 0.11157 0.72801 0.74367 0.47492 0.47366 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   United States 2017-03-08 Pharyngula Embryo Undetermined Embryo Imprecise
41890 41890 SRR5320519 SRX2619924 SRS2029887 SRP101558 PRJNA378498 Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development GSE95812 Transcriptome Analysis Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.   pubmed:28705894   WT fli1a 2 GSM2526398   tissue:Mixed/Vaculature|developmental stage:36 hpf|genotype:WT|treatment:N1 WT fli1a 2 Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample Mixed/Vaculature   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   developmental stage:36 hpf|genotype:WT|treatment:N1 GSM2526398 GSM2526398: WT fli1a 2; Danio rerio; RNA Seq GSM2526398   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM2526398 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP101558     GC-802_L000_R1_001.fastq.gz GC-802_L000_R2_001_trimmed.fastq.gz fastq fastq 3350709374.0 22188495.0 GSM2526398 r1 0:76 1:75.11 A:931204481;C:723007023;G:742633449;T:952979264;N:885157 76 75     931204481 723007023 742633449 952979264 885157 SRX2619924 SRS2029887 SRA543392 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.94845 0.94253 0.10164 0.09031 0.75574 0.77323 0.48066 0.47965 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   United States 2017-03-08 Pharyngula Embryo Undetermined Embryo Imprecise
41891 41891 SRR5320518 SRX2619923 SRS2029886 SRP101558 PRJNA378498 Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development GSE95812 Transcriptome Analysis Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.   pubmed:28705894   WT fli1a 1 GSM2526397   tissue:Mixed/Vaculature|developmental stage:36 hpf|genotype:WT|treatment:N1 WT fli1a 1 Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample Mixed/Vaculature   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   developmental stage:36 hpf|genotype:WT|treatment:N1 GSM2526397 GSM2526397: WT fli1a 1; Danio rerio; RNA Seq GSM2526397   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM2526397 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP101558         4801615200.0 48016152.0 GSM2526397 r1 0:50 1:50 A:1295232475;C:1023348546;G:1092265729;T:1389807859;N:960591 50 50     1295232475 1023348546 1092265729 1389807859 960591 SRX2619923 SRS2029886 SRA543392 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.91612 0.73029 0.13929 0.11276 0.74503 0.77147 0.50551 0.49924 50 50 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United States 2017-03-08 Pharyngula Embryo Undetermined Embryo Imprecise
50535 50535 SRR8134458 SRX4955494 SRS3996631 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 3 H24 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_3_R1.fastq H24_3_R2.fastq fastq fastq 1303220750.0 5212883.0 H24 3 R1.fastq 0:125 1:125 A:353042196;C:298548859;G:299882991;T:351742904;N:3800 125 125     353042196 298548859 299882991 351742904 3800 SRX4955494 SRS3996631 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.95284 0.94903 0.03485 0.03522 0.8606 0.86168 0.49556 0.49795 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50536 50536 SRR8134459 SRX4955493 SRS3996630 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 1 H24 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_1_R1.fastq H24_1_R2.fastq fastq fastq 1040367750.0 4161471.0 H24 1 R1.fastq 0:125 1:125 A:285190807;C:235796611;G:237165817;T:282211556;N:2959 125 125     285190807 235796611 237165817 282211556 2959 SRX4955493 SRS3996630 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94648 0.94488 0.0507 0.05253 0.87353 0.87513 0.52936 0.52764 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50537 50537 SRR8134460 SRX4955492 SRS3996629 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 2 H24 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_2_R1.fastq H24_2_R2.fastq fastq fastq 1003243000.0 4012972.0 H24 2 R1.fastq 0:125 1:125 A:275192369;C:227024454;G:228346661;T:272676506;N:3010 125 125     275192369 227024454 228346661 272676506 3010 SRX4955492 SRS3996629 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94467 0.94348 0.06361 0.06541 0.8423 0.84478 0.51257 0.51745 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50616 50616 SRR8182176 SRX5002143 SRS4036806 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 36hpf RNA seq rep2 GSM3467126   tissue:Soma 36hpf RNA seq replicate 2|cell type:somatic cells|developmental stage:36hpf Soma 36hpf RNA seq rep2 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. Soma 36hpf RNA seq replicate 2   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:36hpf GSM3467126 GSM3467126: Soma 36hpf RNA seq rep2; Danio rerio; RNA Seq GSM3467126   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467126 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_36h_rep2_R1.fastq.gz Soma_36h_rep2_R2.fastq.gz fastq fastq 9552191554.0 47288077.0 GSM3467126 r1 0:101 1:101 A:1826573622;C:2930484284;G:2973076939;T:1821467438;N:589271 101 101     1826573622 2930484284 2973076939 1821467438 589271 SRX5002143 SRS4036806 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.97325 0.97248 0.23454 0.23626 0.82473 0.82501 0.75685 0.80207 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Pharyngula Embryo Undetermined Embryo Imprecise
50617 50617 SRR8182175 SRX5002142 SRS4036805 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 36hpf RNA seq rep1 GSM3467125   tissue:Soma 36hpf RNA seq replicate 1|cell type:somatic cells|developmental stage:36hpf Soma 36hpf RNA seq rep1 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. Soma 36hpf RNA seq replicate 1   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:36hpf GSM3467125 GSM3467125: Soma 36hpf RNA seq rep1; Danio rerio; RNA Seq GSM3467125   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_36h_rep1_R1.fastq.gz Soma_36h_rep1_R2.fastq.gz fastq fastq 11057427278.0 54739739.0 GSM3467125 r1 0:101 1:101 A:2176624694;C:3328344416;G:3373884891;T:2177880530;N:692747 101 101     2176624694 3328344416 3373884891 2177880530 692747 SRX5002142 SRS4036805 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.96735 0.96743 0.23647 0.23809 0.81375 0.8146 0.70848 0.67456 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Pharyngula Embryo Undetermined Embryo Imprecise
50618 50618 SRR8182174 SRX5002141 SRS4036804 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 24hpf RNA seq rep2 GSM3467124   tissue:Soma 24hpf RNA seq replicate 2|cell type:somatic cells|developmental stage:24hpf Soma 24hpf RNA seq rep2 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. Soma 24hpf RNA seq replicate 2   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:24hpf GSM3467124 GSM3467124: Soma 24hpf RNA seq rep2; Danio rerio; RNA Seq GSM3467124   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467124 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_24h_rep2_R1.fastq.gz Soma_24h_rep2_R2.fastq.gz fastq fastq 10189379344.0 50442472.0 GSM3467124 r1 0:101 1:101 A:1868726340;C:3202324778;G:3239656806;T:1878040678;N:630742 101 101     1868726340 3202324778 3239656806 1878040678 630742 SRX5002141 SRS4036804 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.97951 0.97958 0.21009 0.21166 0.8424 0.84374 0.76765 0.80617 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Pharyngula Embryo Undetermined Embryo Imprecise
50619 50619 SRR8182173 SRX5002140 SRS4036803 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 24hpf RNA seq rep1 GSM3467123   tissue:PGCs 24hpf RNA seq replicate 1|cell type:somatic cells|developmental stage:24hpf Soma 24hpf RNA seq rep1 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. PGCs 24hpf RNA seq replicate 1   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:24hpf GSM3467123 GSM3467123: Soma 24hpf RNA seq rep1; Danio rerio; RNA Seq GSM3467123   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467123 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_24h_rep1_R1.fastq.gz Soma_24h_rep1_R2.fastq.gz fastq fastq 10253700386.0 50760893.0 GSM3467123 r1 0:101 1:101 A:1908514410;C:3198046674;G:3227993553;T:1918507136;N:638613 101 101     1908514410 3198046674 3227993553 1918507136 638613 SRX5002140 SRS4036803 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.97536 0.97489 0.23104 0.22906 0.83327 0.83427 0.77755 0.80859 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Pharyngula Embryo Undetermined Embryo Imprecise
51716 51716 SRR8799033 SRX5587876 SRS4549123 SRP189741 PRJNA529645 Retention of paternal epigenetic memory in the developing teleost germline [alt splicing] GSE128986 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: In order to perform alternative splicing analysis PGC 7 hpf PGC 24 hpf Soma 7 hpf and Soma 24 hpf low input RNA seq samples have been sequenced on an additional lane of Nova seq 6000 and analyzed together with the previous RNA seq run GSE122480. parent bioproject:PRJNA506076 pubmed:31296860   Soma 24hpf RNA seq rep2 RUN2 GSM3689560   tissue:Soma 24hpf RNA seq replicate 2 RUN2|cell type:somatic cells|developmental stage:24hpf Soma 24hpf RNA seq rep2 RUN2 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 2 developmental stages in replicates. Soma 24hpf RNA seq replicate 2 RUN2   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:24hpf GSM3689560 GSM3689560: Soma 24hpf RNA seq rep2 RUN2; Danio rerio; RNA Seq GSM3689560   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3689560 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP189741     Soma_24h_rep2_R1_001.fastq.gz Soma_24h_rep2_R2_001.fastq.gz fastq fastq 20883504976.0 103383688.0 GSM3689560 r1 0:101 1:101 A:3777932937;C:6606274257;G:6691850017;T:3807345376;N:102389 101 101     3777932937 6606274257 6691850017 3807345376 102389 SRX5587876 SRS4549123 SRA867175 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.98041 0.98076 0.20416 0.2099 0.8439 0.84508 0.78759 0.77091 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2019-03-28 Pharyngula Embryo Undetermined Embryo Imprecise
51717 51717 SRR8799032 SRX5587875 SRS4549122 SRP189741 PRJNA529645 Retention of paternal epigenetic memory in the developing teleost germline [alt splicing] GSE128986 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: In order to perform alternative splicing analysis PGC 7 hpf PGC 24 hpf Soma 7 hpf and Soma 24 hpf low input RNA seq samples have been sequenced on an additional lane of Nova seq 6000 and analyzed together with the previous RNA seq run GSE122480. parent bioproject:PRJNA506076 pubmed:31296860   Soma 24hpf RNA seq rep1 RUN2 GSM3689559   tissue:Soma 24hpf RNA seq replicate 1 RUN2|cell type:somatic cells|developmental stage:24hpf Soma 24hpf RNA seq rep1 RUN2 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 2 developmental stages in replicates. Soma 24hpf RNA seq replicate 1 RUN2   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:24hpf GSM3689559 GSM3689559: Soma 24hpf RNA seq rep1 RUN2; Danio rerio; RNA Seq GSM3689559   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3689559 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP189741     Soma_24h_rep1_R2_001.fastq.gz Soma_24h_rep1_R1_001.fastq.gz fastq fastq 19299181202.0 95540501.0 GSM3689559 r1 0:101 1:101 A:3543331187;C:6057844778;G:6126196452;T:3571713395;N:95390 101 101     3543331187 6057844778 6126196452 3571713395 95390 SRX5587875 SRS4549122 SRA867175 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.97724 0.97713 0.22611 0.22739 0.83786 0.83733 0.81906 0.82862 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2019-03-28 Pharyngula Embryo Undetermined Embryo Imprecise
69604 69604 SRR18935955 SRX15013551 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81332 L81332 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-2_L7_I332.R1.clean.fastq.gz fastq 3448675800.0 22991172.0 Alad 2 L7 I332.R1.clean.fastq.gz 0:150 1:0 A:909204217;C:819708757;G:815883274;T:903292138;N:587414 150 0     909204217 819708757 815883274 903292138 587414 SRX15013551 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93973   0.13997   0.7685   0.51168   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69605 69605 SRR18935956 SRX15013550 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81331 L81331 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-1_L8_I331.R1.clean.fastq.gz fastq 3987610500.0 26584070.0 Alad 1 L8 I331.R1.clean.fastq.gz 0:150 1:0 A:1031398922;C:974521107;G:967367126;T:1013951504;N:371841 150 0     1031398922 974521107 967367126 1013951504 371841 SRX15013550 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.9447   0.1019   0.81286   0.58316   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69606 69606 SRR18935957 SRX15013549 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81330 L81330 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-2_L8_I330.R1.clean.fastq.gz fastq 4163915100.0 27759434.0 Alas2 2 L8 I330.R1.clean.fastq.gz 0:150 1:0 A:1119245849;C:968636914;G:967111308;T:1108544148;N:376881 150 0     1119245849 968636914 967111308 1108544148 376881 SRX15013549 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.92608   0.1778   0.75471   0.55161   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69607 69607 SRR18935958 SRX15013548 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81329 L81329 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-1_L8_I329.R1.clean.fastq.gz fastq 3953391150.0 26355941.0 Alas2 1 L8 I329.R1.clean.fastq.gz 0:150 1:0 A:1035309566;C:950958591;G:946245209;T:1020520823;N:356961 150 0     1035309566 950958591 946245209 1020520823 356961 SRX15013548 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93024   0.14212   0.81213   0.61442   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69608 69608 SRR18935959 SRX15013547 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81328 L81328 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-2_L8_I328.R1.clean.fastq.gz fastq 3589015200.0 23926768.0 WT 2 L8 I328.R1.clean.fastq.gz 0:150 1:0 A:922300230;C:887849832;G:879590696;T:898942142;N:332300 150 0     922300230 887849832 879590696 898942142 332300 SRX15013547 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94576   0.09241   0.83514   0.68592   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69609 69609 SRR18935960 SRX15013546 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81327 L81327 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-1_L8_I327.R1.clean.fastq.gz fastq 4062851700.0 27085678.0 WT 1 L8 I327.R1.clean.fastq.gz 0:150 1:0 A:1028410873;C:1020911876;G:1010215515;T:1002940085;N:373351 150 0     1028410873 1020911876 1010215515 1002940085 373351 SRX15013546 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94919   0.0692   0.85567   0.70156   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise

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