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6 rows where devstage_curation = "Undetermined" and devstage_curation_coarse = "Juvenile"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Juvenile · 6 ✖

devstage_curation 1

  • Undetermined · 6 ✖
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
25267 25267 SRR25744342 SRX21467662 SRS18702380 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 3 GSM7730282   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730282 GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq GSM7730282 r1 GSM7730282 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz fastq fastq 2170738056.0 10746228.0 GSM7730282 r1 0:101 1:101 A:531993767;C:520631008;G:565772072;T:552334154;N:7055 101 101     531993767 520631008 565772072 552334154 7055 SRX21467662 SRS18702380 SRA1698764 IMP IMP 2 0.77665 0.7702 0.14988 0.14284 0.66716 0.66957 0.49991 0.47425 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25268 25268 SRR25744343 SRX21467661 SRS18702379 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 2 GSM7730281   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730281 GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq GSM7730281 r1 GSM7730281 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz fastq fastq 3459149000.0 17124500.0 GSM7730281 r1 0:101 1:101 A:876732239;C:796603142;G:882912604;T:902886783;N:14232 101 101     876732239 796603142 882912604 902886783 14232 SRX21467661 SRS18702379 SRA1698764 IMP IMP 2 0.81761 0.79589 0.26282 0.24746 0.70607 0.7039 0.50658 0.49236 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25269 25269 SRR25744344 SRX21467660 SRS18702381 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 1 GSM7730280   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730280 GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq GSM7730280 r1 GSM7730280 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz fastq fastq 2189781202.0 10840501.0 GSM7730280 r1 0:101 1:101 A:537591255;C:525448020;G:568979980;T:557754770;N:7177 101 101     537591255 525448020 568979980 557754770 7177 SRX21467660 SRS18702381 SRA1698764 IMP IMP 2 0.7459 0.74191 0.15778 0.15291 0.65543 0.65841 0.48578 0.48291 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25270 25270 SRR25744345 SRX21467659 SRS18702378 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 3 GSM7730279   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730279 GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq GSM7730279 r1 GSM7730279 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz fastq fastq 3674041448.0 18188324.0 GSM7730279 r1 0:101 1:101 A:910831144;C:876967044;G:953299105;T:932928913;N:15242 101 101     910831144 876967044 953299105 932928913 15242 SRX21467659 SRS18702378 SRA1698764 IMP IMP 2 0.89093 0.89038 0.09253 0.09348 0.73892 0.73858 0.47115 0.47218 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25271 25271 SRR25744346 SRX21467658 SRS18702377 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 2 GSM7730278   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730278 GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq GSM7730278 r1 GSM7730278 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz fastq fastq 3024886370.0 14974685.0 GSM7730278 r1 0:101 1:101 A:744374909;C:727299396;G:782294774;T:770904797;N:12494 101 101     744374909 727299396 782294774 770904797 12494 SRX21467658 SRS18702377 SRA1698764 IMP IMP 2 0.91806 0.91689 0.06949 0.07178 0.74458 0.74474 0.47548 0.47338 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25272 25272 SRR25744347 SRX21467657 SRS18702376 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 1 GSM7730277   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730277 GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq GSM7730277 r1 GSM7730277 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz fastq fastq 3571638356.0 17681378.0 GSM7730277 r1 0:101 1:101 A:876280472;C:856417516;G:935896746;T:903028845;N:14777 101 101     876280472 856417516 935896746 903028845 14777 SRX21467657 SRS18702376 SRA1698764 IMP IMP 2 0.89559 0.89353 0.09223 0.09423 0.73052 0.73012 0.47772 0.47408 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System

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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");;