{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation = \"Multi-tissue\"", "rows": [[51, "DRR029943", "DRX026961", "DRS086501", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "oocyte maturation duirng natural paring", "zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq]", "SAMD00025433", null, "sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025433", "DRX026961", "5 OM", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025433", null, null, null, 573617016.0, 15933806.0, "DRR029943", "0:36", "A:130606804;C:141376330;G:145891720;T:155734276;N:7886", 36, null, null, null, 130606804, 141376330, 145891720, 155734276, 7886, "DRX026961", "DRS086501", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91108, null, 0.0173, null, 0.76205, null, 0.46319, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Multi-tissue", "Multi-system"], [168, "DRR075402", "DRX069316", "DRS075497", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The liver of tumor fish 7dpf", "Tumor liver", "SAMD00065416", null, "sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065416", "DRX069316", "Tumor liver", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065416", null, null, null, 1091167236.0, 30310201.0, "DRR075402", "0:36", "A:272216839;C:257523620;G:259746158;T:301642763;N:37856", 36, null, null, null, 272216839, 257523620, 259746158, 301642763, 37856, "DRX069316", "DRS075497", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.90443, null, 0.08935, null, 0.71863, null, 0.51145, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Multi-tissue", "Multi-system"], [169, "DRR075401", "DRX069315", "DRS075496", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The gut of tumor fish 7dpf", "Tumor gut", "SAMD00065415", null, "sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065415", "DRX069315", "Tumor gut", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065415", null, null, null, 1423792872.0, 39549802.0, "DRR075401", "0:36", "A:342328685;C:346616167;G:341519547;T:393278536;N:49937", 36, null, null, null, 342328685, 346616167, 341519547, 393278536, 49937, "DRX069315", "DRS075496", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.91303, null, 0.0869, null, 0.70494, null, 0.44332, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Multi-tissue", "Multi-system"], [170, "DRR075400", "DRX069314", "DRS075495", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The remaining part of body of tumor fish 7dpf", "Tumor body", "SAMD00065414", null, "sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065414", "DRX069314", "Tumor body", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065414", null, null, null, 1168514964.0, 32458749.0, "DRR075400", "0:36", "A:286579925;C:275496498;G:278133055;T:328265078;N:40408", 36, null, null, null, 286579925, 275496498, 278133055, 328265078, 40408, "DRX069314", "DRS075495", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.89927, null, 0.15051, null, 0.66714, null, 0.47579, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Multi-tissue", "Multi-system"], [175, "DRR084197", "DRX078028", "DRS086522", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2]", "SAMD00073604", null, "sample name:M 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073604", "DRX078028", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073604", null, null, null, 1389837888.0, 38606608.0, "DRR084197", "0:36", "A:320671418;C:336948866;G:347550258;T:381720581;N:2946765", 36, null, null, null, 320671418, 336948866, 347550258, 381720581, 2946765, "DRX078028", "DRS086522", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.89763, null, 0.02235, null, 0.76445, null, 0.46381, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [181, "DRR084191", "DRX078022", "DRS086516", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1]", "SAMD00073598", null, "sample name:M|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073598", "DRX078022", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<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>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073598", null, null, null, 1050981012.0, 29193917.0, "DRR084191", "0:36", "A:241048832;C:256186268;G:260277071;T:293299597;N:169244", 36, null, null, null, 241048832, 256186268, 260277071, 293299597, 169244, "DRX078022", "DRS086516", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.9088, null, 0.02369, null, 0.7624, null, 0.47998, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [36271, "SRR298568", "SRX079846", "SRS212652", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "ZiwiIPTes", "GSM727525", null, "tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL", "ZiwiIPTes", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Ziwi antibody in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727525", "GSM727525: ZiwiIPTes", "GSM727525: ZiwiIPTes", "GSM727525: ZiwiIPTes", "1", null, "GEO Accession:GSM727525", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<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>", "SRP007331", null, "read name barcode proc directive:ignore", "ZiwiIPTes.fastq", "fastq", 976120596.0, 27114461.0, "GSM727525 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079846", "SRS212652", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.10415, null, 0.03658, null, 0.96173, null, 0.30033, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36276, "SRR298563", "SRX079841", "SRS212647", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "TDRD1IPshort", "GSM727520", null, "tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL", "TDRD1IPshort", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727520", "GSM727520: TDRD1IPshort", "GSM727520: TDRD1IPshort", "GSM727520: TDRD1IPshort", "1", null, "GEO Accession:GSM727520", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<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>", "SRP007331", null, "read name barcode proc directive:ignore", "TDRD1IPshort.fastq", "fastq", 957724884.0, 26603469.0, "GSM727520 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079841", "SRS212647", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.10539, null, 0.05124, null, 0.93935, null, 0.34909, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36277, "SRR298562", "SRX079840", "SRS212646", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "TDRD1IPlong", "GSM727519", null, "tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL", "TDRD1IPlong", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 \u00c2\u00b5l.  For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727519", "GSM727519: TDRD1IPlong", "GSM727519: TDRD1IPlong", "GSM727519: TDRD1IPlong", "1", null, "GEO Accession:GSM727519", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</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>", "SRP007331", null, "read name barcode proc directive:ignore", "TDRD1IPlong.fastq", "fastq", 1098157770.0, 23872995.0, "GSM727519 1", "0:46", null, 46, null, null, null, null, null, null, null, null, "SRX079840", "SRS212646", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.63282, null, 0.29001, null, 0.80095, null, 0.51046, null, 46, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36560, "SRR1048073", "SRX363298", "SRS369337", "SRP016132", "PRJNA177642", "Danio rerio Transcriptome or Gene expression", "PRJNA177642", "Other", "Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.", null, null, "Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.", "Zebrafish pineal gland", "Pineal gland", null, null, null, null, null, null, null, null, null, null, "Zebrafish Brain miRNA", "Brain miRNA", "1", "Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer\u2019s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer\u2019s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP016132", null, null, "ZB_trimmed.fastq", "fastq", 323899236.0, 14781569.0, "Brain miRNA run", "0:21.91 1:0", "A:77705253;C:63882329;G:85902986;T:96383552;N:25116", 21, 0, null, null, 77705253, 63882329, 85902986, 96383552, 25116, "SRX363298", "SRS369337", "SRA054264", "Tel Aviv University", "Tel Aviv University", 1, 0.88754, null, 0.06569, null, 0.96747, null, 0.53358, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Israel", "2015-07-22", "Adult", "Adult", "Multi-tissue", "Multi-system"], [36561, "SRR1048072", "SRX363297", "SRS369337", "SRP016132", "PRJNA177642", "Danio rerio Transcriptome or Gene expression", "PRJNA177642", "Other", "Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.", null, null, "Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.", "Zebrafish pineal gland", "Pineal gland", null, null, null, null, null, null, null, null, null, null, "Zebrafish pineal gland dark miRNA", "Pineal gland dark miRNA", "1", "Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer\u2019s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer\u2019s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP016132", null, null, "D_trimmed.fastq", "fastq", 231371620.0, 10385264.0, "Pineal gland dark miRNA run", "0:22.28 1:0", "A:61228408;C:44264639;G:58700027;T:67159878;N:18668", 22, 0, null, null, 61228408, 44264639, 58700027, 67159878, 18668, "SRX363297", "SRS369337", "SRA054264", "Tel Aviv University", "Tel Aviv University", 1, 0.84648, null, 0.04467, null, 0.95645, null, 0.79978, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Israel", "2015-07-22", "Adult", "Adult", "Multi-tissue", "Multi-system"], [36562, "SRR1048071", "SRX363296", "SRS369337", "SRP016132", "PRJNA177642", "Danio rerio Transcriptome or Gene expression", "PRJNA177642", "Other", "Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.", null, null, "Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.", "Zebrafish pineal gland", "Pineal gland", null, null, null, null, null, null, null, null, null, null, "Zebrafish pineal gland light miRNA", "Pineal gland light miRNA", "1", "Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For miR seq  18 pineal glands were pooled from the 6 sampling times for both light and dark treatments  and one brain pool was composed of 4 brains that were collected from light  and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen.  miRNA capturing and library construction  for the pineal light  pineal dark and brain samples  were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer\u2019s protocol. Briefly  three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx  then five prime adapter was added using T4 RNA Ligase with ATP. postwards  reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally  gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries pineal light  pineal dark  and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer\u2019s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. The total number of reads post filtering was 6 million  10.4 million and 14.8 million for the pineal light  pineal dark and brain  respectively.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP016132", null, null, "L_trimmed.fastq", "fastq", 132417471.0, 5933638.0, "Pineal gland light miRNA run", "0:22.32 1:0", "A:36017069;C:26569684;G:32546616;T:37273526;N:10576", 22, 0, null, null, 36017069, 26569684, 32546616, 37273526, 10576, "SRX363296", "SRS369337", "SRA054264", "Tel Aviv University", "Tel Aviv University", 1, 0.86427, null, 0.03426, null, 0.95631, null, 0.86509, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Israel", "2015-07-22", "Adult", "Adult", "Multi-tissue", "Multi-system"], [36707, "SRR835172", "SRX271968", "SRS416264", "SRP021517", "PRJNA198908", "Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin", "GSE46387", "Transcriptome Analysis", "In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing", null, "pubmed:23874447", null, "il 97h 42 440", "GSM1129630", null, "tissue:iridophores|hpf", "il 97h 42 440", "Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library", "iridophores", null, "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129630", "GSM1129630: il 97h 42 440; Danio rerio; RNA Seq", "GSM1129630 1", null, "1", "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129630", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "il_97h_42_440.fq.bz2", "fastq", 113120952.0, 2693356.0, "GSM1129630 r1", "0:42", "A:26578283;C:27647612;G:26417805;T:32470133;N:7119", 42, null, null, null, 26578283, 27647612, 26417805, 32470133, 7119, "SRX271968", "SRS416264", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.85151, null, 0.08761, null, 0.85766, null, 0.53122, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Multi-tissue", "Multi-system"], [36708, "SRR835171", "SRX271967", "SRS416263", "SRP021517", "PRJNA198908", "Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin", "GSE46387", "Transcriptome Analysis", "In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing", null, "pubmed:23874447", null, "il 77h 49 440", "GSM1129629", null, "tissue:iridophores|hpf", "il 77h 49 440", "Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library", "iridophores", null, "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129629", "GSM1129629: il 77h 49 440; Danio rerio; RNA Seq", "GSM1129629 1", null, "1", "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129629", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "il_77h_49_440.fq.bz2", "fastq", 119102886.0, 2835783.0, "GSM1129629 r1", "0:42", "A:27449590;C:27743213;G:26605006;T:37297547;N:7530", 42, null, null, null, 27449590, 27743213, 26605006, 37297547, 7530, "SRX271967", "SRS416263", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.85274, null, 0.12109, null, 0.86239, null, 0.52589, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Multi-tissue", "Multi-system"], [36709, "SRR835170", "SRX271966", "SRS416261", "SRP021517", "PRJNA198908", "Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin", "GSE46387", "Transcriptome Analysis", "In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing", null, "pubmed:23874447", null, "il 77h 44 440", "GSM1129628", null, "tissue:iridophores|hpf", "il 77h 44 440", "Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library", "iridophores", null, "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129628", "GSM1129628: il 77h 44 440; Danio rerio; RNA Seq", "GSM1129628 1", null, "1", "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129628", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "il_77h_44_440.fq.bz2", "fastq", 319536210.0, 7608005.0, "GSM1129628 r1", "0:42", "A:72602262;C:81003831;G:76662728;T:89248984;N:18405", 42, null, null, null, 72602262, 81003831, 76662728, 89248984, 18405, "SRX271966", "SRS416261", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.88506, null, 0.08161, null, 0.85756, null, 0.50585, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Multi-tissue", "Multi-system"], [36710, "SRR835169", "SRX271965", "SRS416262", "SRP021517", "PRJNA198908", "Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin", "GSE46387", "Transcriptome Analysis", "In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing", null, "pubmed:23874447", null, "il 77h 38 351", "GSM1129627", null, "tissue:iridophores|hpf", "il 77h 38 351", "Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library", "iridophores", null, "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129627", "GSM1129627: il 77h 38 351; Danio rerio; RNA Seq", "GSM1129627 1", null, "1", "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129627", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "il_77h_38_351_AGTGT.fq.bz2", "fastq", 105470208.0, 2929728.0, "GSM1129627 r1", "0:36", "A:23660397;C:24772356;G:27192539;T:29844080;N:836", 36, null, null, null, 23660397, 24772356, 27192539, 29844080, 836, "SRX271965", "SRS416262", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.76356, null, 0.07685, null, 0.86634, null, 0.51592, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Multi-tissue", "Multi-system"], [36711, "SRR835168", "SRX271964", "SRS416260", "SRP021517", "PRJNA198908", "Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin", "GSE46387", "Transcriptome Analysis", "In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing", null, "pubmed:23874447", null, "il 58h 50 440", "GSM1129626", null, "tissue:iridophores|hpf", "il 58h 50 440", "Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library", "iridophores", null, "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", null, "hpf", "GSM1129626", "GSM1129626: il 58h 50 440; Danio rerio; RNA Seq", "GSM1129626 1", null, "1", "This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25\u00b0C in mitfavc7.  When held at 32\u00b0C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25\u00b0C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37\u00b0C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37\u00b0C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4\u00b0C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4\u00b0C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400\u00b5L of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4\u00b0C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4\u00b0C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100\u00b5L containing the pigment cell pellet.  Cells were resuspended with 50\u00b5L of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500\u00b5L of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500\u00b5L cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1\u00b5m or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads\u00ae mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3\u2019 end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.", "GEO Accession:GSM1129626", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021517", null, null, "il_58h_50_440.fq.bz2", "fastq", 158731692.0, 3779326.0, "GSM1129626 r1", "0:42", "A:35358330;C:37377423;G:36834086;T:49152866;N:8987", 42, null, null, null, 35358330, 37377423, 36834086, 49152866, 8987, "SRX271964", "SRS416260", "SRA074390", "GEO", "Rob Mitra, Genetics, Washington University", 1, 0.78748, null, 0.04211, null, 0.88183, null, 0.51498, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-25", "Larval", "Larval", "Multi-tissue", "Multi-system"], [40439, "SRR3144620", "SRX1560771", "SRS1275344", "SRP069287", "PRJNA310829", "Danio rerio strain:AB Raw sequence reads", "PRJNA310829", "Other", "transcriptional profile of both macrophages M and endothelial end cells EC between three different lesion stages uninjured control con  upon macrophage arrival arr  and during macrophage traction tra.", null, null, null, null, "macrophage and endothelial cells", null, "strain:AB|age:Day3|sex:not determined|tissue:macrophage and endothelial cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "macrophage and endothelial cells", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "SRP069287", null, null, "EC-con-2-27_1.fq.gz", "fastq", 2627841170.0, 26309124.0, "macrophages and endothelial cells", "0:99.88 1:0", "A:787503280;C:537314192;G:533698336;T:769265722;N:59640", 99, 0, null, null, 787503280, 537314192, 533698336, 769265722, 59640, "SRX1560771", "SRS1275344", "SRA347117", "SouthWest university Of China|Laboratory of Molecular Developmental Biology", "Southwest University of China", 1, 0.87616, null, 0.42753, null, 0.88477, null, 0.63864, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-02-23", "Larval", "Larval", "Multi-tissue", "Multi-system"], [40947, "SRR3465556", "SRX1735458", "SRS1416510", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X14 tumor", "GSM2136824", null, "source name:brain tumor|tissue:brain tumor", "9267X14 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136824", "GSM2136824: 9267X14 tumor; Danio rerio; RNA Seq", "GSM2136824", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136824", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X14_120613_SN141_0510_AC0TF4ACXX_8.txt.gz", "fastq", 1403474100.0, 28069482.0, "GSM2136824 r1", "0:50", "A:379029580;C:327462448;G:316163138;T:380761095;N:57839", 50, null, null, null, 379029580, 327462448, 316163138, 380761095, 57839, "SRX1735458", "SRS1416510", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.91779, null, 0.10471, null, 0.68018, null, 0.46831, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40948, "SRR3465555", "SRX1735457", "SRS1416511", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X13 tumor", "GSM2136823", null, "source name:brain tumor|tissue:brain tumor", "9267X13 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136823", "GSM2136823: 9267X13 tumor; Danio rerio; RNA Seq", "GSM2136823", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136823", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X13_120613_SN141_0510_AC0TF4ACXX_8.txt.gz", "fastq", 1055273100.0, 21105462.0, "GSM2136823 r1", "0:50", "A:284702255;C:246805964;G:238397873;T:285323357;N:43651", 50, null, null, null, 284702255, 246805964, 238397873, 285323357, 43651, "SRX1735457", "SRS1416511", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.92157, null, 0.09143, null, 0.73494, null, 0.47743, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40949, "SRR3465554", "SRX1735456", "SRS1416509", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X12 tumor", "GSM2136822", null, "source name:brain tumor|tissue:brain tumor", "9267X12 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136822", "GSM2136822: 9267X12 tumor; Danio rerio; RNA Seq", "GSM2136822", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136822", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X12_120613_SN141_0510_AC0TF4ACXX_8.txt.gz", "fastq", 1235405300.0, 24708106.0, "GSM2136822 r1", "0:50", "A:334940379;C:286734309;G:278305987;T:335374199;N:50426", 50, null, null, null, 334940379, 286734309, 278305987, 335374199, 50426, "SRX1735456", "SRS1416509", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.91587, null, 0.10088, null, 0.68107, null, 0.48664, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40950, "SRR3465553", "SRX1735455", "SRS1416508", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X8 tumor", "GSM2136821", null, "source name:brain tumor|tissue:brain tumor", "9267X8 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136821", "GSM2136821: 9267X8 tumor; Danio rerio; RNA Seq", "GSM2136821", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136821", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X8_120613_SN141_0510_AC0TF4ACXX_7.txt.gz", "fastq", 1049619800.0, 20992396.0, "GSM2136821 r1", "0:50", "A:284508112;C:243447832;G:236471909;T:285153684;N:38263", 50, null, null, null, 284508112, 243447832, 236471909, 285153684, 38263, "SRX1735455", "SRS1416508", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.92111, null, 0.10635, null, 0.68061, null, 0.48665, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40951, "SRR3465552", "SRX1735454", "SRS1416507", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X7 tumor", "GSM2136820", null, "source name:brain tumor|tissue:brain tumor", "9267X7 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136820", "GSM2136820: 9267X7 tumor; Danio rerio; RNA Seq", "GSM2136820", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X7_120613_SN141_0510_AC0TF4ACXX_7.txt.gz", "fastq", 1050373350.0, 21007467.0, "GSM2136820 r1", "0:50", "A:283795799;C:244445968;G:237807604;T:284286043;N:37936", 50, null, null, null, 283795799, 244445968, 237807604, 284286043, 37936, "SRX1735454", "SRS1416507", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.91684, null, 0.09541, null, 0.70808, null, 0.4782, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40952, "SRR3465551", "SRX1735453", "SRS1416506", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X6 tumor", "GSM2136819", null, "source name:brain tumor|tissue:brain tumor", "9267X6 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136819", "GSM2136819: 9267X6 tumor; Danio rerio; RNA Seq", "GSM2136819", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X6_120613_SN141_0510_AC0TF4ACXX_7.txt.gz", "fastq", 909187300.0, 18183746.0, "GSM2136819 r1", "0:50", "A:246296969;C:211315305;G:203857359;T:247684298;N:33369", 50, null, null, null, 246296969, 211315305, 203857359, 247684298, 33369, "SRX1735453", "SRS1416506", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.92029, null, 0.11221, null, 0.68578, null, 0.47422, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [40953, "SRR3465550", "SRX1735452", "SRS1416505", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X5 tumor", "GSM2136818", null, "source name:brain tumor|tissue:brain tumor", "9267X5 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136818", "GSM2136818: 9267X5 tumor; Danio rerio; RNA Seq", "GSM2136818", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X5_120613_SN141_0510_AC0TF4ACXX_7.txt.gz", "fastq", 1030064550.0, 20601291.0, "GSM2136818 r1", "0:50", "A:275570887;C:242993408;G:235025540;T:276437064;N:37651", 50, null, null, null, 275570887, 242993408, 235025540, 276437064, 37651, "SRX1735452", "SRS1416505", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.91852, null, 0.0986, null, 0.70451, null, 0.47961, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [41035, "SRR3581677", "SRX1797273", "SRS1465195", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages4", "iRed4", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed4", "iRed4", "iRed4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed4.fastq.gz", "fastq", 2577391029.0, 50537079.0, "iRed4.fastq.gz", "0:51", "A:740368299;C:555561208;G:558570747;T:722870515;N:20260", 51, null, null, null, 740368299, 555561208, 558570747, 722870515, 20260, "SRX1797273", "SRS1465195", "SRA429040", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.87886, null, 0.09748, null, 0.75676, null, 0.49364, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-05-25", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41036, "SRR3581675", "SRX1797272", "SRS1465194", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages3", "iRed3", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed3", "iRed3", "iRed3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed3.fastq.gz", "fastq", 2300094339.0, 45099889.0, "iRed3.fastq.gz", "0:51", "A:664396273;C:491535578;G:495836023;T:648307877;N:18588", 51, null, null, null, 664396273, 491535578, 495836023, 648307877, 18588, "SRX1797272", "SRS1465194", "SRA429039", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.88281, null, 0.15449, null, 0.75507, null, 0.47198, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41037, "SRR3581674", "SRX1797271", "SRS1465193", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages2", "iRed2", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed2", "iRed2", "iRed2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed2.fastq.gz", "fastq", 1652550807.0, 32402957.0, "iRed2.fastq.gz", "0:51", "A:528348867;C:306088006;G:305625547;T:512475625;N:12762", 51, null, null, null, 528348867, 306088006, 305625547, 512475625, 12762, "SRX1797271", "SRS1465193", "SRA429038", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.83699, null, 0.16858, null, 0.76688, null, 0.49036, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-05-25", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41363, "SRR4369389", "SRX2224020", "SRS1731682", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3", "GSM2339156", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339156", "GSM2339156: 4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq", "GSM2339156", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ243.fq.gz", "fastq", 1057994900.0, 21159898.0, "GSM2339156 r1", "0:50", "A:280437817;C:246195249;G:248543608;T:282775343;N:42883", 50, null, null, null, 280437817, 246195249, 248543608, 282775343, 42883, "SRX2224020", "SRS1731682", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.92441, null, 0.07101, null, 0.73259, null, 0.53564, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41364, "SRR4369388", "SRX2224018", "SRS1731680", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3", "GSM2339155", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339155", "GSM2339155: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq", "GSM2339155", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ213.fq.gz", "fastq", 1192895250.0, 23857905.0, "GSM2339155 r1", "0:50", "A:311520729;C:281518333;G:288563950;T:311243358;N:48880", 50, null, null, null, 311520729, 281518333, 288563950, 311243358, 48880, "SRX2224018", "SRS1731680", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.92622, null, 0.06398, null, 0.7315, null, 0.51969, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41365, "SRR4369387", "SRX2224017", "SRS1731679", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae low fat cohort rep3", "GSM2339154", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae low fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339154", "GSM2339154: Unfed 6.5 dpf zebrafish larvae low fat cohort rep3; Danio rerio; RNA Seq", "GSM2339154", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ203.fq.gz", "fastq", 1333885750.0, 26677715.0, "GSM2339154 r1", "0:50", "A:350227472;C:314164789;G:317046609;T:352393122;N:53758", 50, null, null, null, 350227472, 314164789, 317046609, 352393122, 53758, "SRX2224017", "SRS1731679", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.92695, null, 0.07507, null, 0.72675, null, 0.54558, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41366, "SRR4369386", "SRX2224016", "SRS1731677", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3", "GSM2339153", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339153", "GSM2339153: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq", "GSM2339153", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339153", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ143.fq.gz", "fastq", 3620501750.0, 72410035.0, "GSM2339153 r1", "0:50", "A:928100369;C:870292711;G:888545580;T:933466612;N:96478", 50, null, null, null, 928100369, 870292711, 888545580, 933466612, 96478, "SRX2224016", "SRS1731677", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93833, null, 0.05511, null, 0.75032, null, 0.55771, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41367, "SRR4369385", "SRX2224015", "SRS1731678", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3", "GSM2339152", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339152", "GSM2339152: 1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq", "GSM2339152", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339152", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ113.fq.gz", "fastq", 2177871950.0, 43557439.0, "GSM2339152 r1", "0:50", "A:563893287;C:522092755;G:523081504;T:568747495;N:56909", 50, null, null, null, 563893287, 522092755, 523081504, 568747495, 56909, "SRX2224015", "SRS1731678", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93698, null, 0.06235, null, 0.75335, null, 0.53049, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41368, "SRR4369384", "SRX2224014", "SRS1731676", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae high fat cohort rep3", "GSM2339151", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae high fat cohort rep3", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339151", "GSM2339151: Unfed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq", "GSM2339151", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339151", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ103.fq.gz", "fastq", 1451132900.0, 29022658.0, "GSM2339151 r1", "0:50", "A:377007117;C:346007409;G:346873642;T:381206074;N:38658", 50, null, null, null, 377007117, 346007409, 346873642, 381206074, 38658, "SRX2224014", "SRS1731676", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93743, null, 0.06292, null, 0.74241, null, 0.53805, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41369, "SRR4369383", "SRX2224013", "SRS1731675", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2", "GSM2339150", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339150", "GSM2339150: 4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq", "GSM2339150", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339150", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ242.fq.gz", "fastq", 1989936500.0, 39798730.0, "GSM2339150 r1", "0:50", "A:523392551;C:467800437;G:470494505;T:528201420;N:47587", 50, null, null, null, 523392551, 467800437, 470494505, 528201420, 47587, "SRX2224013", "SRS1731675", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93233, null, 0.07279, null, 0.72987, null, 0.54632, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41370, "SRR4369382", "SRX2224012", "SRS1731674", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2", "GSM2339149", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339149", "GSM2339149: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq", "GSM2339149", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339149", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ212.fq.gz", "fastq", 2625058500.0, 52501170.0, "GSM2339149 r1", "0:50", "A:685255578;C:619614827;G:635559034;T:684566225;N:62836", 50, null, null, null, 685255578, 619614827, 635559034, 684566225, 62836, "SRX2224012", "SRS1731674", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93545, null, 0.06765, null, 0.74399, null, 0.53905, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41371, "SRR4369381", "SRX2224011", "SRS1731672", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae low fat cohort rep2", "GSM2339148", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae low fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339148", "GSM2339148: Unfed 6.5 dpf zebrafish larvae low fat cohort rep2; Danio rerio; RNA Seq", "GSM2339148", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339148", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ202.fq.gz", "fastq", 1339075850.0, 26781517.0, "GSM2339148 r1", "0:50", "A:350406690;C:316421667;G:317254683;T:354961605;N:31205", 50, null, null, null, 350406690, 316421667, 317254683, 354961605, 31205, "SRX2224011", "SRS1731672", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93323, null, 0.07254, null, 0.7307, null, 0.55068, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41372, "SRR4369380", "SRX2224010", "SRS1731671", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2", "GSM2339147", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339147", "GSM2339147: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2; Danio rerio; RNA Seq", "GSM2339147", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339147", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ142.fq.gz", "fastq", 1286162750.0, 25723255.0, "GSM2339147 r1", "0:50", "A:346299275;C:294122420;G:300696019;T:345003487;N:41549", 50, null, null, null, 346299275, 294122420, 300696019, 345003487, 41549, "SRX2224010", "SRS1731671", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.9281, null, 0.07755, null, 0.7305, null, 0.53462, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41373, "SRR4369379", "SRX2224009", "SRS1731673", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2", "GSM2339146", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339146", "GSM2339146: 1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2; Danio rerio; RNA Seq", "GSM2339146", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339146", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ112.fq.gz", "fastq", 2002111100.0, 40042222.0, "GSM2339146 r1", "0:50", "A:528562099;C:471825161;G:473013263;T:528647491;N:63086", 50, null, null, null, 528562099, 471825161, 473013263, 528647491, 63086, "SRX2224009", "SRS1731673", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93335, null, 0.07285, null, 0.7419, null, 0.54916, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41374, "SRR4369378", "SRX2224008", "SRS1731670", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae high fat cohort rep2", "GSM2339145", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae high fat cohort rep2", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339145", "GSM2339145: Unfed 6.5 dpf zebrafish larvae high fat cohort rep2; Danio rerio; RNA Seq", "GSM2339145", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ102.fq.gz", "fastq", 1273490300.0, 25469806.0, "GSM2339145 r1", "0:50", "A:331637156;C:303754192;G:304976628;T:333081790;N:40534", 50, null, null, null, 331637156, 303754192, 304976628, 333081790, 40534, "SRX2224008", "SRS1731670", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93565, null, 0.07655, null, 0.74249, null, 0.54451, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41375, "SRR4369377", "SRX2224007", "SRS1731669", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "GSM2339144", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339144", "GSM2339144: 4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1; Danio rerio; RNA Seq", "GSM2339144", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339144", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ241.fq.gz", "fastq", 2211365050.0, 44227301.0, "GSM2339144 r1", "0:50", "A:569415166;C:531526907;G:533692966;T:576677396;N:52615", 50, null, null, null, 569415166, 531526907, 533692966, 576677396, 52615, "SRX2224007", "SRS1731669", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93633, null, 0.06376, null, 0.73701, null, 0.55588, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41376, "SRR4369376", "SRX2224006", "SRS1731668", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "GSM2339143", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339143", "GSM2339143: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1; Danio rerio; RNA Seq", "GSM2339143", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339143", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ211.fq.gz", "fastq", 2627126000.0, 52542520.0, "GSM2339143 r1", "0:50", "A:679161674;C:624785100;G:633592207;T:689524385;N:62634", 50, null, null, null, 679161674, 624785100, 633592207, 689524385, 62634, "SRX2224006", "SRS1731668", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93885, null, 0.06121, null, 0.74629, null, 0.53653, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41377, "SRR4369375", "SRX2224005", "SRS1731667", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae low fat cohort rep1", "GSM2339142", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae low fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339142", "GSM2339142: Unfed 6.5 dpf zebrafish larvae low fat cohort rep1; Danio rerio; RNA Seq", "GSM2339142", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ201.fq.gz", "fastq", 2356799900.0, 47135998.0, "GSM2339142 r1", "0:50", "A:604464780;C:566235047;G:573048901;T:612995653;N:55519", 50, null, null, null, 604464780, 566235047, 573048901, 612995653, 55519, "SRX2224005", "SRS1731667", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93799, null, 0.06151, null, 0.7419, null, 0.54342, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41378, "SRR4369374", "SRX2224004", "SRS1731666", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1", "GSM2339141", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339141", "GSM2339141: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1; Danio rerio; RNA Seq", "GSM2339141", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ141.fq.gz", "fastq", 2314803100.0, 46296062.0, "GSM2339141 r1", "0:50", "A:608880073;C:542117358;G:554834849;T:608902370;N:68450", 50, null, null, null, 608880073, 542117358, 554834849, 608902370, 68450, "SRX2224004", "SRS1731666", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.9381, null, 0.06487, null, 0.74974, null, 0.53946, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41379, "SRR4369373", "SRX2224003", "SRS1731665", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1", "GSM2339140", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339140", "GSM2339140: 1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1; Danio rerio; RNA Seq", "GSM2339140", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ111.fq.gz", "fastq", 1178777050.0, 23575541.0, "GSM2339140 r1", "0:50", "A:309227949;C:279025719;G:278433554;T:312055796;N:34032", 50, null, null, null, 309227949, 279025719, 278433554, 312055796, 34032, "SRX2224003", "SRS1731665", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.9381, null, 0.06761, null, 0.74882, null, 0.54735, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [41380, "SRR4369372", "SRX2224002", "SRS1731664", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "Unfed 6.5 dpf zebrafish larvae high fat cohort rep1", "GSM2339139", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "Unfed 6.5 dpf zebrafish larvae high fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339139", "GSM2339139: Unfed 6.5 dpf zebrafish larvae high fat cohort rep1; Danio rerio; RNA Seq", "GSM2339139", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ101.fq.gz", "fastq", 1628978050.0, 32579561.0, "GSM2339139 r1", "0:50", "A:426504328;C:384692513;G:386557023;T:431176784;N:47402", 50, null, null, null, 426504328, 384692513, 386557023, 431176784, 47402, "SRX2224002", "SRS1731664", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93781, null, 0.06883, null, 0.73959, null, 0.52987, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-system"], [48792, "SRR7299187", "SRX4201621", "SRS3411855", "SRP150378", "PRJNA475809", "Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq", "GSE115719", "Transcriptome Analysis", "Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1  transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor10b", "GSM3188303", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor10b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", null, "strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "GSM3188303", "GSM3188303: Tumor10b; Danio rerio; RNA Seq", "GSM3188303", null, "1", "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", "GEO Accession:GSM3188303", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP150378", null, null, "P2_11_CCGTCC_L002_R1_001.fastq.gz", "fastq", 777639687.0, 15247837.0, "GSM3188303 r1", "0:51 1:0", "A:207311416;C:184430035;G:177791849;T:208055451;N:50936", 51, 0, null, null, 207311416, 184430035, 177791849, 208055451, 50936, "SRX4201621", "SRS3411855", "SRA720941", "GEO", "Maura McGrail, GDCB, Iowa State University", 1, 0.90266, null, 0.11487, null, 0.70485, null, 0.48043, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-12", "Adult", "Adult", "Multi-tissue", "Multi-system"], [48793, "SRR7299186", "SRX4201620", "SRS3411854", "SRP150378", "PRJNA475809", "Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq", "GSE115719", "Transcriptome Analysis", "Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1  transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor10a", "GSM3188302", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor10a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", null, "strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "GSM3188302", "GSM3188302: Tumor10a; Danio rerio; RNA Seq", "GSM3188302", null, "1", "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", "GEO Accession:GSM3188302", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP150378", null, null, "P1_11_CCGTCC_L001_R1_001.fastq.gz", "fastq", 668178132.0, 13101532.0, "GSM3188302 r1", "0:51 1:0", "A:177845565;C:158702532;G:152983178;T:178607700;N:39157", 51, 0, null, null, 177845565, 158702532, 152983178, 178607700, 39157, "SRX4201620", "SRS3411854", "SRA720941", "GEO", "Maura McGrail, GDCB, Iowa State University", 1, 0.8996, null, 0.11677, null, 0.7079, null, 0.47973, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-12", "Adult", "Adult", "Multi-tissue", "Multi-system"], [48794, "SRR7299185", "SRX4201619", "SRS3411853", "SRP150378", "PRJNA475809", "Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq", "GSE115719", "Transcriptome Analysis", "Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1  transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor9b", "GSM3188301", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor9b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", null, "strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "GSM3188301", "GSM3188301: Tumor9b; Danio rerio; RNA Seq", "GSM3188301", null, "1", "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", "GEO Accession:GSM3188301", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP150378", null, null, "P2_10_ATGTCA_L002_R1_001.fastq.gz", "fastq", 702134340.0, 13767340.0, "GSM3188301 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX4201619", "SRS3411853", "SRA720941", "GEO", "Maura McGrail, GDCB, Iowa State University", 1, 0.90571, null, 0.14513, null, 0.69203, null, 0.47889, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-12", "Adult", "Adult", "Multi-tissue", "Multi-system"], [48795, "SRR7299184", "SRX4201618", "SRS3411852", "SRP150378", "PRJNA475809", "Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq", "GSE115719", "Transcriptome Analysis", "Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1  transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor9a", "GSM3188300", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor9a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor8b", "GSM3188299", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor8b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor8a", "GSM3188298", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor8a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor7b", "GSM3188297", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor7b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor7a", "GSM3188296", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor7a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor6b", "GSM3188295", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor6b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor6a", "GSM3188294", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor6a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor5b", "GSM3188293", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor5b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor4b", "GSM3188291", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor4b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor3b", "GSM3188289", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor3b", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. 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FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", null, "strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "GSM3188285", "GSM3188285: Tumor1b; Danio rerio; RNA Seq", "GSM3188285", null, "1", "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", "GEO Accession:GSM3188285", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP150378", null, null, "P2_02_CGATGT_L002_R1_001.fastq.gz", "fastq", 784768773.0, 15387623.0, "GSM3188285 r1", "0:51 1:0", "A:208146136;C:186789193;G:180795319;T:208985840;N:52285", 51, 0, null, null, 208146136, 186789193, 180795319, 208985840, 52285, "SRX4201603", "SRS3411836", "SRA720941", "GEO", "Maura McGrail, GDCB, Iowa State University", 1, 0.90541, null, 0.10585, null, 0.71056, null, 0.47843, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-12", "Adult", "Adult", "Multi-tissue", "Multi-system"], [48811, "SRR7299168", "SRX4201602", "SRS3411837", "SRP150378", "PRJNA475809", "Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq", "GSE115719", "Transcriptome Analysis", "Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1  transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 /  mutant transcriptome  to identify molecular pathways that distinguish transformed rb1  tumor cells from non transformed rb1 /  mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month.", "parent bioproject:PRJNA475805", "pubmed:29914980", null, "Tumor1a", "GSM3188284", null, "source name:Brain tumor tissue|strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "Tumor1a", "Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters \u201c N 1  t 8  B 4  m 5  A sam   split output\u201d. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics.", "Brain tumor tissue", null, "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", null, "strain/background:WIK|genotype:rb1  TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor", "GSM3188284", "GSM3188284: Tumor1a; Danio rerio; RNA Seq", "GSM3188284", null, "1", "Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.", "GEO Accession:GSM3188284", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP150378", null, null, "P1_02_CGATGT_L001_R1_001.fastq.gz", "fastq", 718085304.0, 14080104.0, "GSM3188284 r1", "0:51 1:0", "A:190524485;C:171176089;G:164179700;T:192161274;N:43756", 51, 0, null, null, 190524485, 171176089, 164179700, 192161274, 43756, "SRX4201602", "SRS3411837", "SRA720941", "GEO", "Maura McGrail, GDCB, Iowa State University", 1, 0.90155, null, 0.10675, null, 0.71019, null, 0.47991, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-12", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53027, "SRR9669993", "SRX6430480", "SRS5085640", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample6 zic ras tert TR rep3", "GSM3937766", null, "tissue:Adult brain tumor|treatment:zic UAS:tert;UAS:TR inj ras", "Sample6 zic ras tert TR rep3", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic UAS:tert;UAS:TR inj ras", "GSM3937766", "GSM3937766: Sample6 zic ras tert TR rep3; Danio rerio; RNA Seq", "GSM3937766", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937766", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N6_AI_6_zic_ras_tert_TR_3_S6_R1.fastq.gz", "fastq", 1779340129.0, 17617229.0, "GSM3937766 r1", "0:101 1:0", "A:530371091;C:316769511;G:405002707;T:527096600;N:100220", 101, 0, null, null, 530371091, 316769511, 405002707, 527096600, 100220, "SRX6430480", "SRS5085640", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.81386, null, 0.19286, null, 0.79066, null, 0.58782, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53028, "SRR9669992", "SRX6430479", "SRS5085639", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample5 zic ras tert TR rep2", "GSM3937765", null, "tissue:Adult brain tumor|treatment:zic UAS:tert;UAS:TR inj ras", "Sample5 zic ras tert TR rep2", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic UAS:tert;UAS:TR inj ras", "GSM3937765", "GSM3937765: Sample5 zic ras tert TR rep2; Danio rerio; RNA Seq", "GSM3937765", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937765", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N5_AI_5_zic_ras_tert_TR_2_S5_R1.fastq.gz", "fastq", 1818179881.0, 18001781.0, "GSM3937765 r1", "0:101 1:0", "A:540242623;C:321875714;G:418515128;T:537443873;N:102543", 101, 0, null, null, 540242623, 321875714, 418515128, 537443873, 102543, "SRX6430479", "SRS5085639", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.81011, null, 0.1708, null, 0.79194, null, 0.58047, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53029, "SRR9669991", "SRX6430478", "SRS5085638", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample4 zic ras tert TR rep1", "GSM3937764", null, "tissue:Adult brain tumor|treatment:zic UAS:tert;UAS:TR inj ras", "Sample4 zic ras tert TR rep1", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic UAS:tert;UAS:TR inj ras", "GSM3937764", "GSM3937764: Sample4 zic ras tert TR rep1; Danio rerio; RNA Seq", "GSM3937764", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937764", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N4_AI_4_zic_ras_tert_TR_1_S4_R1.fastq.gz", "fastq", 1918498939.0, 18995039.0, "GSM3937764 r1", "0:101 1:0", "A:587524426;C:339600798;G:441683287;T:549584233;N:106195", 101, 0, null, null, 587524426, 339600798, 441683287, 549584233, 106195, "SRX6430478", "SRS5085638", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.77512, null, 0.18858, null, 0.80673, null, 0.59479, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53030, "SRR9669990", "SRX6430477", "SRS5085637", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample3 zic ras rep3", "GSM3937763", null, "tissue:Adult brain tumor|treatment:zic inj ras", "Sample3 zic ras rep3", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic inj ras", "GSM3937763", "GSM3937763: Sample3 zic ras rep3; Danio rerio; RNA Seq", "GSM3937763", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937763", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N3_AI_3_zic_ras_3_S3_R1.fastq.gz", "fastq", 1803775463.0, 17859163.0, "GSM3937763 r1", "0:101 1:0", "A:546840565;C:325717348;G:423849705;T:507266868;N:100977", 101, 0, null, null, 546840565, 325717348, 423849705, 507266868, 100977, "SRX6430477", "SRS5085637", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.80869, null, 0.14118, null, 0.81097, null, 0.59204, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53031, "SRR9669989", "SRX6430476", "SRS5085636", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample2 zic ras rep2", "GSM3937762", null, "tissue:Adult brain tumor|treatment:zic inj ras", "Sample2 zic ras rep2", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic inj ras", "GSM3937762", "GSM3937762: Sample2 zic ras rep2; Danio rerio; RNA Seq", "GSM3937762", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937762", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N2_AI_2_zic_ras_2_S2_R1.fastq.gz", "fastq", 1994074613.0, 19743313.0, "GSM3937762 r1", "0:101 1:0", "A:606290106;C:355481454;G:458919131;T:573271976;N:111946", 101, 0, null, null, 606290106, 355481454, 458919131, 573271976, 111946, "SRX6430476", "SRS5085636", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.80311, null, 0.14529, null, 0.80016, null, 0.61351, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [53032, "SRR9669988", "SRX6430475", "SRS5085635", "SRP214202", "PRJNA554016", "Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.", "GSE134135", "Transcriptome Analysis", "The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres  senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM   but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here  we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally  tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length  with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer  we performed RNA sequencing analysis RNA Seq  of the transcriptome of two zebrafish models of brain cancer  one ALT+ and the other telomerase+.", null, null, null, "Sample1 zic ras rep1", "GSM3937761", null, "tissue:Adult brain tumor|treatment:zic inj ras", "Sample1 zic ras rep1", "Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al.  2013  version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample", "Adult brain tumor", "One of the two groups of samples overexpress also telomerase through the Gal4/UAS system", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer\u2019s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "Brain tumors were induced in developing zebrafish through the Gal4/UAS system  using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid", "treatment:zic inj ras", "GSM3937761", "GSM3937761: Sample1 zic ras rep1; Danio rerio; RNA Seq", "GSM3937761", null, "1", "RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.", "GEO Accession:GSM3937761", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N1_AI_1_zic_ras_1_S1_R1.fastq.gz", "fastq", 1840262925.0, 18220425.0, "GSM3937761 r1", "0:101 1:0", "A:541527209;C:334145158;G:434769924;T:529718084;N:102550", 101, 0, null, null, 541527209, 334145158, 434769924, 529718084, 102550, "SRX6430475", "SRS5085635", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.83576, null, 0.15359, null, 0.79555, null, 0.59782, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59351, "SRR11862874", "SRX8413250", "SRS6725560", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchE", "library 10 batchE stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:10SMALL GTTTCG L002 R1 001.fastq.gz|batch:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchE", "10SMALL GTTTCG L002 R1 001.fastq.gz", "10SMALL GTTTCG L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "10SMALL_GTTTCG_L002_R1_001.fastq.gz", "fastq", 610892898.0, 9255953.0, "10SMALL GTTTCG L002 R1 001.fastq.gz", "0:66", "A:131858438;C:155399854;G:158242625;T:165382769;N:9212", 66, null, null, null, 131858438, 155399854, 158242625, 165382769, 9212, "SRX8413250", "SRS6725560", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.07236, null, 0.0163, null, 0.95574, null, 0.71914, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59352, "SRR11862875", "SRX8413249", "SRS6725559", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchE", "library 9 batchE control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:9SMALL GTGGCC L002 R1 001.fastq.gz|batch:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchE", "9SMALL GTGGCC L002 R1 001.fastq.gz", "9SMALL GTGGCC L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "9SMALL_GTGGCC_L002_R1_001.fastq.gz", "fastq", 681019152.0, 10318472.0, "9SMALL GTGGCC L002 R1 001.fastq.gz", "0:66", "A:145919628;C:180332988;G:185160654;T:169595863;N:10019", 66, null, null, null, 145919628, 180332988, 185160654, 169595863, 10019, "SRX8413249", "SRS6725559", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.03361, null, 0.00721, null, 0.97585, null, 0.72421, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59353, "SRR11862876", "SRX8413248", "SRS6725558", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchD", "library 8 batchD stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:8SMALL GTGAAA L002 R1 001.fastq.gz|batch:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchD", "8SMALL GTGAAA L002 R1 001.fastq.gz", "8SMALL GTGAAA L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "8SMALL_GTGAAA_L002_R1_001.fastq.gz", "fastq", 881814912.0, 13360832.0, "8SMALL GTGAAA L002 R1 001.fastq.gz", "0:66", "A:223839245;C:210712788;G:239626812;T:207623100;N:12967", 66, null, null, null, 223839245, 210712788, 239626812, 207623100, 12967, "SRX8413248", "SRS6725558", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.01456, null, 0.00285, null, 0.98685, null, 0.79954, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59354, "SRR11862877", "SRX8413247", "SRS6725557", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchD", "library 7 batchD control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:7SMALL GTCCGC L002 R1 001.fastq.gz|batch:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchD", "7SMALL GTCCGC L002 R1 001.fastq.gz", "7SMALL GTCCGC L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "7SMALL_GTCCGC_L002_R1_001.fastq.gz", "fastq", 871937682.0, 13211177.0, "7SMALL GTCCGC L002 R1 001.fastq.gz", "0:66", "A:187309754;C:240910478;G:236157154;T:207547961;N:12335", 66, null, null, null, 187309754, 240910478, 236157154, 207547961, 12335, "SRX8413247", "SRS6725557", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.00388, null, 0.00062, null, 0.99622, null, 0.86525, null, 66, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59355, "SRR11862878", "SRX8413246", "SRS6725556", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchC", "library 6 batchC stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:6SMALL GTAGAG L002 R1 001.fastq.gz|batch:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchC", "6SMALL GTAGAG L002 R1 001.fastq.gz", "6SMALL GTAGAG L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "6SMALL_GTAGAG_L002_R1_001.fastq.gz", "fastq", 588357594.0, 8914509.0, "6SMALL GTAGAG L002 R1 001.fastq.gz", "0:66", "A:138378307;C:145942814;G:162208729;T:141818898;N:8846", 66, null, null, null, 138378307, 145942814, 162208729, 141818898, 8846, "SRX8413246", "SRS6725556", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.02473, null, 0.00511, null, 0.98317, null, 0.76412, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59356, "SRR11862879", "SRX8413245", "SRS6725555", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchC", "library 5 batchC control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:5SMALL CCGTCC L002 R1 001.fastq.gz|batch:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchC", "5SMALL CCGTCC L002 R1 001.fastq.gz", "5SMALL CCGTCC L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "5SMALL_CCGTCC_L002_R1_001.fastq.gz", "fastq", 724072008.0, 10970788.0, "5SMALL CCGTCC L002 R1 001.fastq.gz", "0:66", "A:153195532;C:210035381;G:176169980;T:184660888;N:10227", 66, null, null, null, 153195532, 210035381, 176169980, 184660888, 10227, "SRX8413245", "SRS6725555", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.02036, null, 0.00355, null, 0.98265, null, 0.71654, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59357, "SRR11862880", "SRX8413244", "SRS6725554", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchB", "library 4 batchB stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:4SMALL ATGTCA L002 R1 001.fastq.gz|batch:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchB", "4SMALL ATGTCA L002 R1 001.fastq.gz", "4SMALL ATGTCA L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "4SMALL_ATGTCA_L002_R1_001.fastq.gz", "fastq", 734716818.0, 11132073.0, "4SMALL ATGTCA L002 R1 001.fastq.gz", "0:66", "A:176688644;C:183414624;G:192032878;T:182569784;N:10888", 66, null, null, null, 176688644, 183414624, 192032878, 182569784, 10888, "SRX8413244", "SRS6725554", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.03816, null, 0.00665, null, 0.97378, null, 0.80915, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59358, "SRR11862881", "SRX8413243", "SRS6725553", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchB", "library 3 batchB control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:3SMALL AGTTCC L002 R1 001.fastq.gz|batch:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchB", "3SMALL AGTTCC L002 R1 001.fastq.gz", "3SMALL AGTTCC L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "3SMALL_AGTTCC_L002_R1_001.fastq.gz", "fastq", 639608178.0, 9691033.0, "3SMALL AGTTCC L002 R1 001.fastq.gz", "0:66", "A:141927022;C:169937693;G:166391833;T:161342157;N:9473", 66, null, null, null, 141927022, 169937693, 166391833, 161342157, 9473, "SRX8413243", "SRS6725553", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.00358, null, 0.00027, null, 0.99857, null, 0.92025, null, 66, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59359, "SRR11862882", "SRX8413242", "SRS6725552", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchF", "library 12 batchF stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:12SMALL GAGTGG L002 R1 001.fastq.gz|batch:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchF", "12SMALL GAGTGG L002 R1 001.fastq.gz", "12SMALL GAGTGG L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "12SMALL_GAGTGG_L002_R1_001.fastq.gz", "fastq", 856789890.0, 12981665.0, "12SMALL GAGTGG L002 R1 001.fastq.gz", "0:66", "A:197687950;C:209840385;G:245135169;T:204114009;N:12377", 66, null, null, null, 197687950, 209840385, 245135169, 204114009, 12377, "SRX8413242", "SRS6725552", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.13729, null, 0.02049, null, 0.93752, null, 0.71536, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59360, "SRR11862883", "SRX8413241", "SRS6725551", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchF", "library 11 batchF control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:11SMALL CGTACG L002 R1 001.fastq.gz|batch:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchF", "11SMALL CGTACG L002 R1 001.fastq.gz", "11SMALL CGTACG L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "11SMALL_CGTACG_L002_R1_001.fastq.gz", "fastq", 891015576.0, 13500236.0, "11SMALL CGTACG L002 R1 001.fastq.gz", "0:66", "A:215219357;C:226988408;G:230348786;T:218445888;N:13137", 66, null, null, null, 215219357, 226988408, 230348786, 218445888, 13137, "SRX8413241", "SRS6725551", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.10021, null, 0.02466, null, 0.95789, null, 0.65844, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59361, "SRR11862884", "SRX8413240", "SRS6725550", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchA", "library 2 batchA stress", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:2SMALL AGTCAA L002 R1 001.fastq.gz|batch:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from stressed adult male batchA", "2SMALL AGTCAA L002 R1 001.fastq.gz", "2SMALL AGTCAA L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "2SMALL_AGTCAA_L002_R1_001.fastq.gz", "fastq", 790770684.0, 11981374.0, "2SMALL AGTCAA L002 R1 001.fastq.gz", "0:66", "A:198694732;C:195900186;G:206731529;T:189432489;N:11748", 66, null, null, null, 198694732, 195900186, 206731529, 189432489, 11748, "SRX8413240", "SRS6725550", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.06132, null, 0.01001, null, 0.96731, null, 0.807, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59362, "SRR11862885", "SRX8413239", "SRS6725549", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of  zebrafish spermatozoa from control adult male batchA", "library 1 batchA control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:1SMALL CTTGTA L002 R1 001.fastq.gz|batch:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of  zebrafish spermatozoa from control adult male batchA", "1SMALL CTTGTA L002 R1 001.fastq.gz", "1SMALL CTTGTA L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "1SMALL_CTTGTA_L002_R1_001.fastq.gz", "fastq", 796394940.0, 12066590.0, "1SMALL CTTGTA L002 R1 001.fastq.gz", "0:66", "A:180861950;C:199407609;G:204723388;T:211390521;N:11472", 66, null, null, null, 180861950, 199407609, 204723388, 211390521, 11472, "SRX8413239", "SRS6725549", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.01922, null, 0.00235, null, 0.99024, null, 0.87449, null, 66, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59501, "SRR11924323", "SRX8469995", "SRS6770646", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Adult tail 2", "GSM4591062", null, "source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "Adult tail 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "adult tail trunk", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591062", "GSM4591062: Adult tail 2; Danio rerio; OTHER", "GSM4591062", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591062", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "Adult_tail_2.bam GSE151797_Reference_sequence.fa", "bam bam", 156647953.0, 5517527.0, "GSM4591062 r1", "0:28.39", "A:32903673;C:49609293;G:39096775;T:35038212;N:0", 28, null, null, null, 32903673, 49609293, 39096775, 35038212, 0, "SRX8469995", "SRS6770646", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.80662, null, 0.20653, null, 0.88722, null, 0.58074, null, 37, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59502, "SRR11924321", "SRX8469994", "SRS6770645", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Adult tail 1", "GSM4591061", null, "source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "Adult tail 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "adult tail trunk", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591061", "GSM4591061: Adult tail 1; Danio rerio; OTHER", "GSM4591061", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591061", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "Adult_tail_1.bam GSE151797_Reference_sequence.fa", "bam bam", 50029636.0, 1968329.0, "GSM4591061 r1", "0:25.42", "A:9571393;C:14825016;G:13276309;T:12356918;N:0", 25, null, null, null, 9571393, 14825016, 13276309, 12356918, 0, "SRX8469994", "SRS6770645", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.46312, null, 0.12127, null, 0.91806, null, 0.67424, null, 44, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Adult", "Adult", "Multi-tissue", "Multi-system"], [67129, "SRR17097015", "SRX13284817", "SRS11197574", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3G S14", "GSM5711820", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3G S14", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711820", "GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq", "GSM5711820", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3G_S14_L001_R1_001.fastq.gz", "fastq", 610454250.0, 8139390.0, "GSM5711820 r1", "0:75 1:0", "A:163825101;C:138603508;G:155901420;T:152120085;N:4136", 75, 0, null, null, 163825101, 138603508, 155901420, 152120085, 4136, "SRX13284817", "SRS11197574", "SRA1337575", "GEO", "US EPA", 1, 0.95929, null, 0.11356, null, 0.72354, null, 0.52498, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67130, "SRR17097016", "SRX13284817", "SRS11197574", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3G S14", "GSM5711820", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3G S14", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711820", "GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq", "GSM5711820", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3G_S14_L002_R1_001.fastq.gz", "fastq", 593213475.0, 7909513.0, "GSM5711820 r2", "0:75 1:0", "A:159210709;C:134719825;G:151432112;T:147848359;N:2470", 75, 0, null, null, 159210709, 134719825, 151432112, 147848359, 2470, "SRX13284817", "SRS11197574", "SRA1337575", "GEO", "US EPA", 1, 0.95964, null, 0.11339, null, 0.72445, null, 0.52239, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67131, "SRR17097017", "SRX13284817", "SRS11197574", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3G S14", "GSM5711820", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3G S14", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711820", "GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq", "GSM5711820", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3G_S14_L003_R1_001.fastq.gz", "fastq", 599448525.0, 7992647.0, "GSM5711820 r3", "0:75 1:0", "A:160858296;C:136155437;G:153190178;T:149240819;N:3795", 75, 0, null, null, 160858296, 136155437, 153190178, 149240819, 3795, "SRX13284817", "SRS11197574", "SRA1337575", "GEO", "US EPA", 1, 0.95904, null, 0.11412, null, 0.72533, null, 0.5151, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67132, "SRR17097018", "SRX13284817", "SRS11197574", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3G S14", "GSM5711820", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3G S14", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711820", "GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq", "GSM5711820", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3G_S14_L004_R1_001.fastq.gz", "fastq", 589356075.0, 7858081.0, "GSM5711820 r4", "0:75 1:0", "A:158219859;C:133806362;G:150430635;T:146895878;N:3341", 75, 0, null, null, 158219859, 133806362, 150430635, 146895878, 3341, "SRX13284817", "SRS11197574", "SRA1337575", "GEO", "US EPA", 1, 0.95902, null, 0.11344, null, 0.72468, null, 0.52555, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67133, "SRR17097011", "SRX13284816", "SRS11197573", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3F S10", "GSM5711819", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3F S10", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711819", "GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq", "GSM5711819", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3F_S10_L001_R1_001.fastq.gz", "fastq", 453579975.0, 6047733.0, "GSM5711819 r1", "0:75 1:0", "A:120833503;C:101700505;G:110413638;T:120555105;N:77224", 75, 0, null, null, 120833503, 101700505, 110413638, 120555105, 77224, "SRX13284816", "SRS11197573", "SRA1337575", "GEO", "US EPA", 1, 0.94667, null, 0.09349, null, 0.70676, null, 0.47641, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67134, "SRR17097012", "SRX13284816", "SRS11197573", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3F S10", "GSM5711819", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3F S10", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711819", "GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq", "GSM5711819", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3F_S10_L002_R1_001.fastq.gz", "fastq", 441645750.0, 5888610.0, "GSM5711819 r2", "0:75 1:0", "A:117659308;C:99057961;G:107463452;T:117396067;N:68962", 75, 0, null, null, 117659308, 99057961, 107463452, 117396067, 68962, "SRX13284816", "SRS11197573", "SRA1337575", "GEO", "US EPA", 1, 0.94671, null, 0.09333, null, 0.70666, null, 0.47464, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67135, "SRR17097013", "SRX13284816", "SRS11197573", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3F S10", "GSM5711819", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3F S10", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711819", "GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq", "GSM5711819", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3F_S10_L003_R1_001.fastq.gz", "fastq", 450520125.0, 6006935.0, "GSM5711819 r3", "0:75 1:0", "A:119957953;C:101154236;G:109745090;T:119627796;N:35050", 75, 0, null, null, 119957953, 101154236, 109745090, 119627796, 35050, "SRX13284816", "SRS11197573", "SRA1337575", "GEO", "US EPA", 1, 0.94629, null, 0.0931, null, 0.70603, null, 0.47769, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67136, "SRR17097014", "SRX13284816", "SRS11197573", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3F S10", "GSM5711819", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3F S10", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711819", "GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq", "GSM5711819", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3F_S10_L004_R1_001.fastq.gz", "fastq", 442567800.0, 5900904.0, "GSM5711819 r4", "0:75 1:0", "A:117881601;C:99242228;G:107863727;T:117545157;N:35087", 75, 0, null, null, 117881601, 99242228, 107863727, 117545157, 35087, "SRX13284816", "SRS11197573", "SRA1337575", "GEO", "US EPA", 1, 0.94519, null, 0.09359, null, 0.7069, null, 0.46281, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67137, "SRR17097007", "SRX13284815", "SRS11197571", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3D S11", "GSM5711818", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3D S11", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711818", "GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq", "GSM5711818", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3D_S11_L001_R1_001.fastq.gz", "fastq", 496347750.0, 6617970.0, "GSM5711818 r1", "0:75 1:0", "A:132860149;C:113519137;G:131829845;T:118135255;N:3364", 75, 0, null, null, 132860149, 113519137, 131829845, 118135255, 3364, "SRX13284815", "SRS11197571", "SRA1337575", "GEO", "US EPA", 1, 0.96017, null, 0.11843, null, 0.74061, null, 0.5142, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67138, "SRR17097008", "SRX13284815", "SRS11197571", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3D S11", "GSM5711818", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3D S11", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711818", "GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq", "GSM5711818", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3D_S11_L002_R1_001.fastq.gz", "fastq", 481482375.0, 6419765.0, "GSM5711818 r2", "0:75 1:0", "A:128841184;C:110129820;G:127873134;T:114636382;N:1855", 75, 0, null, null, 128841184, 110129820, 127873134, 114636382, 1855, "SRX13284815", "SRS11197571", "SRA1337575", "GEO", "US EPA", 1, 0.96092, null, 0.12068, null, 0.74036, null, 0.48436, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67139, "SRR17097009", "SRX13284815", "SRS11197571", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3D S11", "GSM5711818", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3D S11", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711818", "GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq", "GSM5711818", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3D_S11_L003_R1_001.fastq.gz", "fastq", 482828025.0, 6437707.0, "GSM5711818 r3", "0:75 1:0", "A:129166672;C:110526807;G:128392727;T:114738937;N:2882", 75, 0, null, null, 129166672, 110526807, 128392727, 114738937, 2882, "SRX13284815", "SRS11197571", "SRA1337575", "GEO", "US EPA", 1, 0.96019, null, 0.1208, null, 0.74132, null, 0.51095, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67140, "SRR17097010", "SRX13284815", "SRS11197571", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3D S11", "GSM5711818", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3D S11", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711818", "GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq", "GSM5711818", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3D_S11_L004_R1_001.fastq.gz", "fastq", 477516825.0, 6366891.0, "GSM5711818 r4", "0:75 1:0", "A:127801747;C:109250038;G:126854910;T:113607491;N:2639", 75, 0, null, null, 127801747, 109250038, 126854910, 113607491, 2639, "SRX13284815", "SRS11197571", "SRA1337575", "GEO", "US EPA", 1, 0.96058, null, 0.12042, null, 0.7403, null, 0.51486, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67141, "SRR17097003", "SRX13284814", "SRS11197572", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3C S8", "GSM5711817", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3C S8", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711817", "GSM5711817: GRC350 D5 3C S8; Danio rerio; RNA Seq", "GSM5711817", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3C_S8_L001_R1_001.fastq.gz", "fastq", 461481525.0, 6153087.0, "GSM5711817 r1", "0:75 1:0", "A:122121827;C:104607471;G:119890528;T:114785157;N:76542", 75, 0, null, null, 122121827, 104607471, 119890528, 114785157, 76542, "SRX13284814", "SRS11197572", "SRA1337575", "GEO", "US EPA", 1, 0.961, null, 0.1222, null, 0.73434, null, 0.52729, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"], [67142, "SRR17097004", "SRX13284814", "SRS11197572", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3C S8", "GSM5711817", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3C S8", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711817", "GSM5711817: GRC350 D5 3C S8; Danio rerio; RNA Seq", "GSM5711817", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3C_S8_L002_R1_001.fastq.gz", "fastq", 452629800.0, 6035064.0, "GSM5711817 r2", "0:75 1:0", "A:119747169;C:102604108;G:117644135;T:112565022;N:69366", 75, 0, null, null, 119747169, 102604108, 117644135, 112565022, 69366, "SRX13284814", "SRS11197572", "SRA1337575", "GEO", "US EPA", 1, 0.96165, null, 0.12333, null, 0.73273, null, 0.52955, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 476, "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": "Multi-tissue"}}, "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=Multi-tissue", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 459, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_strategy=OTHER", "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=Multi-tissue", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "cDNA", "label": "cDNA", "count": 445, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=cDNA", "selected": false}, {"value": "PCR", "label": "PCR", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=PCR", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=size+fractionation", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=RANDOM", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=PolyA", "selected": false}, {"value": "other", "label": "other", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.library_selection=other", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=unknown&tissue_curation=Multi-tissue", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 468, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.platform=BGISEQ", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&experiment.platform=ION_TORRENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "Larval", "label": "Larval", "count": 411, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation_coarse=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation_coarse=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "Larval", "label": "Larval", "count": 411, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation=Undetermined", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation=Pharyngula", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&devstage_curation=Zygote", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "Multi-system", "label": "Multi-system", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&tissue_curation_coarse=Multi-system", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "Multi-tissue", "label": "Multi-tissue", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue", "results": [{"value": "unknown", "label": "unknown", "count": 476, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Multi-tissue", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": "67142", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=unknown&tissue_curation=Multi-tissue&_next=67142", "private": false, "allow_execute_sql": true, "query_ms": 169.51054299715906}