{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation = \"Tail\"", "rows": [[36147, "SRR33446914", "SRX28687233", "SRS24954089", "SRP583344", "PRJNA1259437", "Inhibition of TGF beta signalling during zebrafish larval tail regeneration.", "GSE296469", "Transcriptome Analysis", "This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.", null, null, null, "SB 431542 treated / cut tail replicate 2", "GSM8970920", null, "source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing", "SB 431542 treated / cut tail replicate 2", "demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file", "Larval tail", "SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.", "100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit", "Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40\u2009\u03bcg/ml Tricaine 3 amino benzoic acidethylester in E3. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. 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DMSO was used at 0.1%.", null, null, null, "DMSO treated / cut tail replicate 1", "GSM8970914", null, "source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing", "DMSO treated / cut tail replicate 1", "demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file", "Larval tail", "SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.", "100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit", "Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40\u2009\u03bcg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference", "tissue:Larval tail|genotype:Wild type|treatment:Tail excision", "GSM8970914", "GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq", "GSM8970914 r1", "GSM8970914", "1", "100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP583344", null, null, "Orange-1_S19_L004_R1_001.fastq.gz", "fastq", 351537316.0, 4625491.0, "GSM8970914 r4", "0:76", "A:100573823;C:74441165;G:77263744;T:99256707;N:1877", 76, null, null, null, 100573823, 74441165, 77263744, 99256707, 1877, "SRX28687222", "SRS24954078", "SRA2124571", "University of Sheffield", "University of Sheffield", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2025-05-06", "Larval", "Larval", "Tail", "Multi-system"], [36478, "SRR527835", "SRX171222", "SRS352108", "SRP014596", "PRJNA171539", "Transcriptomic analysis of zebrafish during development and homeostasis", "GSE39703", "Transcriptome Analysis", "Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf  5 day larvae  adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples:  24hpf embryos  pool of 16 hour to 36 hour embryos  5 dpf larvea  adult head and adult tail", null, "pubmed:23684812", null, "tail", "GSM977960", null, "tissue:entire adult tail|genotype:Wild type|strain:AB|Stage:adult tail", "tail", "Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7  options: butterfly search coverage search  microexon search  min anchor length 5   G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options  u  b  M rRNA/Mtgenes mask  G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification", "entire adult tail", null, "Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions", null, "genotype:Wild type|strain:AB|Stage:adult tail", "GSM977960", "GSM977960: tail; Danio rerio; RNA Seq", "GSM977960 1", "GSM977960: tail", "1", null, "GEO Accession:GSM977960", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014596", null, null, null, null, 534897504.0, 14858264.0, "GSM977960 r1", "0:36", "A:144900139;C:122639505;G:130189210;T:136990883;N:177767", 36, null, null, null, 144900139, 122639505, 130189210, 136990883, 177767, "SRX171222", "SRS352108", "SRA056408", "GEO", "ITG", 1, 0.89933, null, 0.04578, null, 0.71254, null, 0.41668, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2012-07-27", "Adult", "Adult", "Tail", "Multi-system"], [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"], [41418, "SRR4423118", "SRX2245302", "SRS1745860", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Adult FT Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: Adult female tail", "172 5", "172 5", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "femaletailRID0172BC05smallZF.fastq", "fastq", 491055734.0, 7690105.0, "femaletailRID0172BC05smallZF.fastq", "0:63.86", "A:114732043;C:132287469;G:130972143;T:113064079;N:0", 63, null, null, null, 114732043, 132287469, 130972143, 113064079, 0, "SRX2245302", "SRS1745860", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.82246, null, 0.13521, null, 0.91303, null, 0.63226, null, 43, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Adult", "Adult", "Tail", "Multi-system"], [41419, "SRR4423117", "SRX2245301", "SRS1745860", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Adult FT Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: Adult female tail", "172 3", "172 3", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "femaletailRID0172BC03largeZF.fastq", "fastq", 1414932187.0, 9757587.0, "femaletailRID0172BC03largeZF.fastq", "0:145.01", "A:343007105;C:362895564;G:422320111;T:286709407;N:0", 145, null, null, null, 343007105, 362895564, 422320111, 286709407, 0, "SRX2245301", "SRS1745860", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.96057, null, 0.21796, null, 0.95177, null, 0.76663, null, 141, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Adult", "Adult", "Tail", "Multi-system"], [63892, "SRR14213374", "SRX10579919", "SRS8684387", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Tail3", "GSM5237143", null, "source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB", "Tail3", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish tail", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:tail|strain:TLAB", "GSM5237143", "GSM5237143: Tail3; Danio rerio; RNA Seq", "GSM5237143", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237143", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Tail3.fastq", "fastq", 1351349800.0, 13513498.0, "GSM5237143 r1", "0:100", "A:344334043;C:321881505;G:312915864;T:372166616;N:51772", 100, null, null, null, 344334043, 321881505, 312915864, 372166616, 51772, "SRX10579919", "SRS8684387", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93634, null, 0.09976, null, 0.75521, null, 0.48801, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Tail", "Multi-system"], [63893, "SRR14213373", "SRX10579918", "SRS8684386", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Tail2", "GSM5237142", null, "source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB", "Tail2", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish tail", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:tail|strain:TLAB", "GSM5237142", "GSM5237142: Tail2; Danio rerio; RNA Seq", "GSM5237142", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Tail2.fastq", "fastq", 1669271300.0, 16692713.0, "GSM5237142 r1", "0:100", "A:422977972;C:402400334;G:387344093;T:456484890;N:64011", 100, null, null, null, 422977972, 402400334, 387344093, 456484890, 64011, "SRX10579918", "SRS8684386", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93177, null, 0.10145, null, 0.75532, null, 0.47775, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Tail", "Multi-system"], [63894, "SRR14213372", "SRX10579917", "SRS8684385", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Tail1", "GSM5237141", null, "source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB", "Tail1", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish tail", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:tail|strain:TLAB", "GSM5237141", "GSM5237141: Tail1; Danio rerio; RNA Seq", "GSM5237141", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Tail1.fastq", "fastq", 2117983600.0, 21179836.0, "GSM5237141 r1", "0:100", "A:534692684;C:517420692;G:497313091;T:568475177;N:81956", 100, null, null, null, 534692684, 517420692, 497313091, 568475177, 81956, "SRX10579917", "SRS8684385", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93316, null, 0.11572, null, 0.74951, null, 0.48824, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Tail", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 66, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "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], [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 from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "unknown", "p2": "Tail"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Tail", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 65, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Tail&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Tail&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Tail", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 66, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Tail&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": 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