{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Pharyngula\" and tissue_curation = \"Tail\"", "rows": [[38049, "SRR1519899", "SRX657112", "SRS662299", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "sih3", "GSM1439473", null, "tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf", "sih3", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:sih|embryonic stage:28 hpf", "GSM1439473", "GSM1439473: sih3; Danio rerio; RNA Seq", "GSM1439473", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-06.fastq.gz", "fastq", 1416036978.0, 26222907.0, "GSM1439473 r1", "0:54", "A:342287675;C:370618836;G:361870457;T:341179934;N:80076", 54, null, null, null, 342287675, 370618836, 361870457, 341179934, 80076, "SRX657112", "SRS662299", "SRA175990", "GEO", "IGBMC", 1, 0.96217, null, 0.03055, null, 0.76869, null, 0.44925, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [38050, "SRR1519898", "SRX657111", "SRS662291", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "WT3", "GSM1439472", null, "tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf", "WT3", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:WT|embryonic stage:28 hpf", "GSM1439472", "GSM1439472: WT3; Danio rerio; RNA Seq", "GSM1439472", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-05.fastq.gz", "fastq", 1787680692.0, 33105198.0, "GSM1439472 r1", "0:54", "A:442553431;C:457003567;G:446438405;T:441598672;N:86617", 54, null, null, null, 442553431, 457003567, 446438405, 441598672, 86617, "SRX657111", "SRS662291", "SRA175990", "GEO", "IGBMC", 1, 0.96318, null, 0.03918, null, 0.75371, null, 0.4423, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [38051, "SRR1519897", "SRX657110", "SRS662290", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "sih2", "GSM1439471", null, "tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf", "sih2", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:sih|embryonic stage:28 hpf", "GSM1439471", "GSM1439471: sih2; Danio rerio; RNA Seq", "GSM1439471", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439471", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-04.fastq.gz", "fastq", 1813069386.0, 33575359.0, "GSM1439471 r1", "0:54", "A:462594376;C:449896725;G:440482879;T:460019095;N:76311", 54, null, null, null, 462594376, 449896725, 440482879, 460019095, 76311, "SRX657110", "SRS662290", "SRA175990", "GEO", "IGBMC", 1, 0.95859, null, 0.05282, null, 0.74199, null, 0.47244, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [38052, "SRR1519896", "SRX657109", "SRS662289", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "WT2", "GSM1439470", null, "tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf", "WT2", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:WT|embryonic stage:28 hpf", "GSM1439470", "GSM1439470: WT2; Danio rerio; RNA Seq", "GSM1439470", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-03.fastq.gz", "fastq", 1866194316.0, 34559154.0, "GSM1439470 r1", "0:54", "A:483946414;C:453986455;G:443561481;T:484623941;N:76025", 54, null, null, null, 483946414, 453986455, 443561481, 484623941, 76025, "SRX657109", "SRS662289", "SRA175990", "GEO", "IGBMC", 1, 0.95615, null, 0.06195, null, 0.73594, null, 0.47144, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [38053, "SRR1519895", "SRX657108", "SRS662288", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "sih1", "GSM1439469", null, "tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf", "sih1", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:sih|embryonic stage:28 hpf", "GSM1439469", "GSM1439469: sih1; Danio rerio; RNA Seq", "GSM1439469", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-02.fastq.gz", "fastq", 1451212470.0, 26874305.0, "GSM1439469 r1", "0:54", "A:368354355;C:360129390;G:353350795;T:369317437;N:60493", 54, null, null, null, 368354355, 360129390, 353350795, 369317437, 60493, "SRX657108", "SRS662288", "SRA175990", "GEO", "IGBMC", 1, 0.94911, null, 0.04509, null, 0.74604, null, 0.46107, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [38054, "SRR1519894", "SRX657107", "SRS662287", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "WT1", "GSM1439468", null, "tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf", "WT1", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:WT|embryonic stage:28 hpf", "GSM1439468", "GSM1439468: WT1; Danio rerio; RNA Seq", "GSM1439468", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C 30 sec at 60\u00b0C 30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439468", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-01.fastq.gz", "fastq", 1583485146.0, 29323799.0, "GSM1439468 r1", "0:54", "A:405051413;C:391145102;G:382645289;T:404569188;N:74154", 54, null, null, null, 405051413, 391145102, 382645289, 404569188, 74154, "SRX657107", "SRS662287", "SRA175990", "GEO", "IGBMC", 1, 0.94743, null, 0.05464, null, 0.73156, null, 0.46572, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41312, "SRR4199307", "SRX2148087", "SRS1679265", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "NICD rep3", "GSM2306087", null, "source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "NICD rep3", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "GSM2306087", "GSM2306087: NICD rep3; Danio rerio; RNA Seq", "GSM2306087", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306087", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "mutant3.fastq.gz", "fastq", 1706861931.0, 33467881.0, "GSM2306087 r1", "0:51 1:0", "A:400027681;C:444926525;G:399939257;T:461913972;N:54496", 51, 0, null, null, 400027681, 444926525, 399939257, 461913972, 54496, "SRX2148087", "SRS1679265", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.75848, null, 0.06958, null, 0.73616, null, 0.47901, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41313, "SRR4199306", "SRX2148086", "SRS1679264", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "NICD rep2", "GSM2306086", null, "source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "NICD rep2", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "GSM2306086", "GSM2306086: NICD rep2; Danio rerio; RNA Seq", "GSM2306086", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "mutant2.fastq.gz", "fastq", 1745551857.0, 34226507.0, "GSM2306086 r1", "0:51 1:0", "A:414724753;C:449494336;G:403529006;T:477747391;N:56371", 51, 0, null, null, 414724753, 449494336, 403529006, 477747391, 56371, "SRX2148086", "SRS1679264", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.77355, null, 0.08842, null, 0.71674, null, 0.48589, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41314, "SRR4199305", "SRX2148085", "SRS1679263", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "NICD rep1", "GSM2306085", null, "source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "NICD rep1", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf", "GSM2306085", "GSM2306085: NICD rep1; Danio rerio; RNA Seq", "GSM2306085", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "mutant1.fastq.gz", "fastq", 1606289064.0, 31495864.0, "GSM2306085 r1", "0:51 1:0", "A:383363329;C:409816147;G:373853062;T:439205035;N:51491", 51, 0, null, null, 383363329, 409816147, 373853062, 439205035, 51491, "SRX2148085", "SRS1679263", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.80199, null, 0.09405, null, 0.71382, null, 0.48651, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41315, "SRR4199304", "SRX2148084", "SRS1679262", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "WT rep3", "GSM2306084", null, "source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "WT rep3", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "GSM2306084", "GSM2306084: WT rep3; Danio rerio; RNA Seq", "GSM2306084", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "WT3.fastq.gz", "fastq", 1621399650.0, 31792150.0, "GSM2306084 r1", "0:51 1:0", "A:394689371;C:400826196;G:384059217;T:441773624;N:51242", 51, 0, null, null, 394689371, 400826196, 384059217, 441773624, 51242, "SRX2148084", "SRS1679262", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.87053, null, 0.08236, null, 0.7218, null, 0.4831, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41316, "SRR4199303", "SRX2148083", "SRS1679261", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "WT rep2", "GSM2306083", null, "source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "WT rep2", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "GSM2306083", "GSM2306083: WT rep2; Danio rerio; RNA Seq", "GSM2306083", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "WT2.fastq.gz", "fastq", 1626903774.0, 31900074.0, "GSM2306083 r1", "0:51 1:0", "A:394214874;C:407655291;G:379120984;T:445859413;N:53212", 51, 0, null, null, 394214874, 407655291, 379120984, 445859413, 53212, "SRX2148083", "SRS1679261", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.81975, null, 0.09539, null, 0.70869, null, 0.4872, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [41317, "SRR4199302", "SRX2148082", "SRS1679260", "SRP087617", "PRJNA342262", "Proliferation independent regulation of organ size by Notch signaling", "GSE86571", "Transcriptome Analysis", "Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.", null, "pubmed:28085667", null, "WT rep1", "GSM2306082", null, "source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "WT rep1", "Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.", "dissociated embryo tails", "Zebrafish embryos positive for GFP were selected.", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.", "strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type", "GSM2306082", "GSM2306082: WT rep1; Danio rerio; RNA Seq", "GSM2306082", null, "1", "Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2306082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP087617", null, null, "WT1.fastq.gz", "fastq", 1646867622.0, 32291522.0, "GSM2306082 r1", "0:51 1:0", "A:400030238;C:412959654;G:377713613;T:456111038;N:53079", 51, 0, null, null, 400030238, 412959654, 377713613, 456111038, 53079, "SRX2148082", "SRS1679260", "SRA464955", "GEO", "Stowers Institute for Medical Research", 1, 0.81411, null, 0.10419, null, 0.70621, null, 0.48075, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-09-08", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69019, "SRR18305957", "SRX14443373", "SRS12250386", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X12", "GSM5949315", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X12", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949315", "GSM5949315: 17656X12; Danio rerio; RNA Seq", "GSM5949315 r1", "GSM5949315", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "12R1.fastq.gz 12R2.fastq.gz", "fastq fastq", 8760074136.0, 29006868.0, "GSM5949315 r1", "0:151 1:151", "A:2225927481;C:2151918912;G:2283765954;T:2098037222;N:424567", 151, 151, null, null, 2225927481, 2151918912, 2283765954, 2098037222, 424567, "SRX14443373", "SRS12250386", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.85829, 0.85613, 0.15473, 0.15346, 0.71192, 0.7161, 0.50878, 0.50915, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69020, "SRR18305958", "SRX14443372", "SRS12250385", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X11", "GSM5949314", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X11", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949314", "GSM5949314: 17656X11; Danio rerio; RNA Seq", "GSM5949314 r1", "GSM5949314", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "11R1.fastq.gz 11R2.fastq.gz", "fastq fastq", 7843778654.0, 25972777.0, "GSM5949314 r1", "0:151 1:151", "A:2038808042;C:1887346702;G:1979694397;T:1937559070;N:370443", 151, 151, null, null, 2038808042, 1887346702, 1979694397, 1937559070, 370443, "SRX14443372", "SRS12250385", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89301, 0.89144, 0.21031, 0.20901, 0.71088, 0.71455, 0.53793, 0.5369, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69021, "SRR18305959", "SRX14443371", "SRS12250384", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X10", "GSM5949313", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X10", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949313", "GSM5949313: 17656X10; Danio rerio; RNA Seq", "GSM5949313 r1", "GSM5949313", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "10R1.fastq.gz 10R2.fastq.gz", "fastq fastq", 7954023150.0, 26337825.0, "GSM5949313 r1", "0:151 1:151", "A:2028488675;C:1961022851;G:2035405718;T:1928722520;N:383386", 151, 151, null, null, 2028488675, 1961022851, 2035405718, 1928722520, 383386, "SRX14443371", "SRS12250384", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.86982, 0.86875, 0.15427, 0.15236, 0.71129, 0.71457, 0.52444, 0.51763, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69022, "SRR18305960", "SRX14443370", "SRS12250383", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X9", "GSM5949312", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X9", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949312", "GSM5949312: 17656X9; Danio rerio; RNA Seq", "GSM5949312 r1", "GSM5949312", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "9R1.fastq.gz 9R2.fastq.gz", "fastq fastq", 7859666572.0, 26025386.0, "GSM5949312 r1", "0:151 1:151", "A:2036985243;C:1891242195;G:1962197484;T:1968861339;N:380311", 151, 151, null, null, 2036985243, 1891242195, 1962197484, 1968861339, 380311, "SRX14443370", "SRS12250383", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89448, 0.89387, 0.17167, 0.16937, 0.70323, 0.70644, 0.49638, 0.49421, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69023, "SRR18305961", "SRX14443369", "SRS12250382", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X8", "GSM5949311", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X8", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949311", "GSM5949311: 17656X8; Danio rerio; RNA Seq", "GSM5949311 r1", "GSM5949311", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "8R1.fastq.gz 8R2.fastq.gz", "fastq fastq", 7557954076.0, 25026338.0, "GSM5949311 r1", "0:151 1:151", "A:2056085755;C:1714978138;G:1811687097;T:1974839053;N:364033", 151, 151, null, null, 2056085755, 1714978138, 1811687097, 1974839053, 364033, "SRX14443369", "SRS12250382", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.90646, 0.90592, 0.22261, 0.22061, 0.69775, 0.70179, 0.47205, 0.47079, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69024, "SRR18305962", "SRX14443368", "SRS12250381", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X7", "GSM5949310", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X7", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949310", "GSM5949310: 17656X7; Danio rerio; RNA Seq", "GSM5949310 r1", "GSM5949310", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "7R1.fastq.gz 7R2.fastq.gz", "fastq fastq", 6353509824.0, 21038112.0, "GSM5949310 r1", "0:151 1:151", "A:1703561525;C:1482787327;G:1549794410;T:1617059845;N:306717", 151, 151, null, null, 1703561525, 1482787327, 1549794410, 1617059845, 306717, "SRX14443368", "SRS12250381", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89285, 0.89264, 0.20804, 0.20747, 0.70098, 0.7038, 0.48387, 0.48103, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69025, "SRR18305963", "SRX14443367", "SRS12250380", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X5", "GSM5949309", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X5", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949309", "GSM5949309: 17656X5; Danio rerio; RNA Seq", "GSM5949309 r1", "GSM5949309", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "5R1.fastq.gz 5R2.fastq.gz", "fastq fastq", 8578103130.0, 28404315.0, "GSM5949309 r1", "0:151 1:151", "A:2316277649;C:1971907307;G:2061501994;T:2228007020;N:409160", 151, 151, null, null, 2316277649, 1971907307, 2061501994, 2228007020, 409160, "SRX14443367", "SRS12250380", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89577, 0.89453, 0.22893, 0.22788, 0.70303, 0.70508, 0.48135, 0.48392, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69026, "SRR18305964", "SRX14443366", "SRS12250379", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X4", "GSM5949308", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "17656X4", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "GSM5949308", "GSM5949308: 17656X4; Danio rerio; RNA Seq", "GSM5949308 r1", "GSM5949308", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "4R1.fastq.gz 4R2.fastq.gz", "fastq fastq", 8433863098.0, 27926699.0, "GSM5949308 r1", "0:151 1:151", "A:2210033640;C:2006122016;G:2101172766;T:2116137389;N:397287", 151, 151, null, null, 2210033640, 2006122016, 2101172766, 2116137389, 397287, "SRX14443366", "SRS12250379", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87323, 0.87203, 0.21174, 0.20953, 0.70668, 0.70989, 0.4827, 0.48242, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69027, "SRR18305965", "SRX14443365", "SRS12250378", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X3", "GSM5949307", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X3", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949307", "GSM5949307: 17656X3; Danio rerio; RNA Seq", "GSM5949307 r1", "GSM5949307", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "3R1.fastq.gz 3R2.fastq.gz", "fastq fastq", 9227012644.0, 30553022.0, "GSM5949307 r1", "0:151 1:151", "A:1700627427;C:2904365136;G:3075918116;T:1545659372;N:442593", 151, 151, null, null, 1700627427, 2904365136, 3075918116, 1545659372, 442593, "SRX14443365", "SRS12250378", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.71833, 0.7183, 0.09555, 0.09613, 0.7848, 0.78756, 0.69573, 0.69937, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69028, "SRR18305966", "SRX14443364", "SRS12250377", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X2", "GSM5949306", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "17656X2", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "GSM5949306", "GSM5949306: 17656X2; Danio rerio; RNA Seq", "GSM5949306 r1", "GSM5949306", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "2R1.fastq.gz 2R2.fastq.gz", "fastq fastq", 9829302418.0, 32547359.0, "GSM5949306 r1", "0:151 1:151", "A:2452313634;C:2455608968;G:2590620889;T:2330290142;N:468785", 151, 151, null, null, 2452313634, 2455608968, 2590620889, 2330290142, 468785, "SRX14443364", "SRS12250377", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87037, 0.86912, 0.17566, 0.17497, 0.71731, 0.72084, 0.51503, 0.5232, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69029, "SRR18305967", "SRX14443363", "SRS12250376", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X1", "GSM5949305", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X1", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts", "tail/posterior to yolk sac", "Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949305", "GSM5949305: 17656X1; Danio rerio; RNA Seq", "GSM5949305 r1", "GSM5949305", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "1R1.fastq.gz 1R2.fastq.gz", "fastq fastq", 8271481926.0, 27389013.0, "GSM5949305 r1", "0:151 1:151", "A:2197036792;C:1943518303;G:2039610176;T:2090922643;N:394012", 151, 151, null, null, 2197036792, 1943518303, 2039610176, 2090922643, 394012, "SRX14443363", "SRS12250376", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87234, 0.87159, 0.21173, 0.21053, 0.70118, 0.70327, 0.46129, 0.45987, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 23, "expanded_columns": [], "expandable_columns": [], 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"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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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], 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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 from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Pharyngula", "p1": "Tail"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&tissue_curation=Tail", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&tissue_curation=Tail&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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