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476 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Multi-tissue"

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experiment.library_selection 7

devstage_curation 5

devstage_curation_coarse 4

experiment.platform 3

experiment.library_strategy 3

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 476 ✖

technology 1

  • unknown · 476 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 476 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
51 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.     oocyte maturation duirng natural paring zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq] SAMD00025433   sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025433 DRX026961 5 OM 1 1   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       573617016.0 15933806.0 DRR029943 0:36 A:130606804;C:141376330;G:145891720;T:155734276;N:7886 36       130606804 141376330 145891720 155734276 7886 DRX026961 DRS086501 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91108   0.0173   0.76205   0.46319   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Multi-tissue Multi-system
168 168 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.     The liver of tumor fish 7dpf Tumor liver SAMD00065416   sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver                 Illumina HiSeq 2500 sequencing of SAMD00065416 DRX069316 Tumor liver 1 Agilent SureSelect Strand Specific RNA Prep Kit   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       1091167236.0 30310201.0 DRR075402 0:36 A:272216839;C:257523620;G:259746158;T:301642763;N:37856 36       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   0.08935   0.71863   0.51145   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
169 169 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.     The gut of tumor fish 7dpf Tumor gut SAMD00065415   sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut                 Illumina HiSeq 2500 sequencing of SAMD00065415 DRX069315 Tumor gut 1 Agilent SureSelect Strand Specific RNA Prep Kit   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       1423792872.0 39549802.0 DRR075401 0:36 A:342328685;C:346616167;G:341519547;T:393278536;N:49937 36       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   0.0869   0.70494   0.44332   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
170 170 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.     The remaining part of body of tumor fish 7dpf Tumor body SAMD00065414   sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body                 Illumina HiSeq 2500 sequencing of SAMD00065414 DRX069314 Tumor body 1 Agilent SureSelect Strand Specific RNA Prep Kit   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       1168514964.0 32458749.0 DRR075400 0:36 A:286579925;C:275496498;G:278133055;T:328265078;N:40408 36       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   0.15051   0.66714   0.47579   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
175 175 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.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] SAMD00073604   sample name:M 4th|replicate:biological replicate 2                 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   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       1389837888.0 38606608.0 DRR084197 0:36 A:320671418;C:336948866;G:347550258;T:381720581;N:2946765 36       320671418 336948866 347550258 381720581 2946765 DRX078028 DRS086522 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89763   0.02235   0.76445   0.46381   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
181 181 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.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] SAMD00073598   sample name:M|replicate:biological replicate 1                 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   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       1050981012.0 29193917.0 DRR084191 0:36 A:241048832;C:256186268;G:260277071;T:293299597;N:169244 36       241048832 256186268 260277071 293299597 169244 DRX078022 DRS086516 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.9088   0.02369   0.7624   0.47998   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
36271 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.   pubmed:21743441   ZiwiIPTes GSM727525   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   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 µl Dynabeads Invitrogen 3 or 6 testes and Ziwi antibody in a total volume of 500 µl. 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.   strain:TL GSM727525 GSM727525: ZiwiIPTes GSM727525: ZiwiIPTes GSM727525: ZiwiIPTes 1   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   read name barcode proc directive:ignore ZiwiIPTes.fastq fastq 976120596.0 27114461.0 GSM727525 1 0:36   36                 SRX079846 SRS212652 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.10415   0.03658   0.96173   0.30033   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Multi-tissue Multi-system
36276 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.   pubmed:21743441   TDRD1IPshort GSM727520   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   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 µl Dynabeads Invitrogen 3 or 6 testes and Tdrd1 antibody 1:100 in a total volume of 500 µl. 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.   strain:TL GSM727520 GSM727520: TDRD1IPshort GSM727520: TDRD1IPshort GSM727520: TDRD1IPshort 1   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   read name barcode proc directive:ignore TDRD1IPshort.fastq fastq 957724884.0 26603469.0 GSM727520 1 0:36   36                 SRX079841 SRS212647 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.10539   0.05124   0.93935   0.34909   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Multi-tissue Multi-system
36277 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.   pubmed:21743441   TDRD1IPlong GSM727519   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   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 µl Dynabeads Invitrogen 3 or 6 testes and Tdrd1 antibody 1:100 in a total volume of 500 µl. 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.   strain:TL GSM727519 GSM727519: TDRD1IPlong GSM727519: TDRD1IPlong GSM727519: TDRD1IPlong 1   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   read name barcode proc directive:ignore TDRD1IPlong.fastq fastq 1098157770.0 23872995.0 GSM727519 1 0:46   46                 SRX079840 SRS212646 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.63282   0.29001   0.80095   0.51046   46   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Multi-tissue Multi-system
36560 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.     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                     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’s 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 …     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     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     77705253 63882329 85902986 96383552 25116 SRX363298 SRS369337 SRA054264 Tel Aviv University Tel Aviv University 1 0.88754   0.06569   0.96747   0.53358   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Israel 2015-07-22 Adult Adult Multi-tissue Multi-system
36561 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.     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                     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’s 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 …     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     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     61228408 44264639 58700027 67159878 18668 SRX363297 SRS369337 SRA054264 Tel Aviv University Tel Aviv University 1 0.84648   0.04467   0.95645   0.79978   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Israel 2015-07-22 Adult Adult Multi-tissue Multi-system
36562 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.     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                     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’s 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 …     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     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     36017069 26569684 32546616 37273526 10576 SRX363296 SRS369337 SRA054264 Tel Aviv University Tel Aviv University 1 0.86427   0.03426   0.95631   0.86509   21   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Israel 2015-07-22 Adult Adult Multi-tissue Multi-system
36707 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   pubmed:23874447   il 97h 42 440 GSM1129630   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   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc…   hpf GSM1129630 GSM1129630: il 97h 42 440; Danio rerio; RNA Seq GSM1129630 1   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc… GEO Accession:GSM1129630 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     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       26578283 27647612 26417805 32470133 7119 SRX271968 SRS416264 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.85151   0.08761   0.85766   0.53122   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Multi-tissue Multi-system
36708 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   pubmed:23874447   il 77h 49 440 GSM1129629   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   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc…   hpf GSM1129629 GSM1129629: il 77h 49 440; Danio rerio; RNA Seq GSM1129629 1   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc… GEO Accession:GSM1129629 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     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       27449590 27743213 26605006 37297547 7530 SRX271967 SRS416263 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.85274   0.12109   0.86239   0.52589   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Multi-tissue Multi-system
36709 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   pubmed:23874447   il 77h 44 440 GSM1129628   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   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc…   hpf GSM1129628 GSM1129628: il 77h 44 440; Danio rerio; RNA Seq GSM1129628 1   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc… GEO Accession:GSM1129628 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     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       72602262 81003831 76662728 89248984 18405 SRX271966 SRS416261 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.88506   0.08161   0.85756   0.50585   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Multi-tissue Multi-system
36710 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   pubmed:23874447   il 77h 38 351 GSM1129627   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   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc…   hpf GSM1129627 GSM1129627: il 77h 38 351; Danio rerio; RNA Seq GSM1129627 1   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc… GEO Accession:GSM1129627 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     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       23660397 24772356 27192539 29844080 836 SRX271965 SRS416262 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.76356   0.07685   0.86634   0.51592   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Multi-tissue Multi-system
36711 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   pubmed:23874447   il 58h 50 440 GSM1129626   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   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc…   hpf GSM1129626 GSM1129626: il 58h 50 440; Danio rerio; RNA Seq GSM1129626 1   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°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C 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°C 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°C 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°C 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°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL 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 000rc… GEO Accession:GSM1129626 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     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       35358330 37377423 36834086 49152866 8987 SRX271964 SRS416260 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.78748   0.04211   0.88183   0.51498   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Multi-tissue Multi-system
40439 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.         macrophage and endothelial cells   strain:AB|age:Day3|sex:not determined|tissue:macrophage and endothelial cells|BioSampleModel:Model organism or animal                 Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction macrophage and endothelial cells 1 1     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     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     787503280 537314192 533698336 769265722 59640 SRX1560771 SRS1275344 SRA347117 SouthWest university Of China|Laboratory of Molecular Developmental Biology Southwest University of China 1 0.87616   0.42753   0.88477   0.63864   100   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-02-23 Larval Larval Multi-tissue Multi-system
40947 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.   pubmed:27783941   9267X14 tumor GSM2136824   source name:brain tumor|tissue:brain tumor 9267X14 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       379029580 327462448 316163138 380761095 57839 SRX1735458 SRS1416510 SRA421168 GEO Oncological Sciences, University of Utah 1 0.91779   0.10471   0.68018   0.46831   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40948 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.   pubmed:27783941   9267X13 tumor GSM2136823   source name:brain tumor|tissue:brain tumor 9267X13 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       284702255 246805964 238397873 285323357 43651 SRX1735457 SRS1416511 SRA421168 GEO Oncological Sciences, University of Utah 1 0.92157   0.09143   0.73494   0.47743   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40949 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.   pubmed:27783941   9267X12 tumor GSM2136822   source name:brain tumor|tissue:brain tumor 9267X12 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       334940379 286734309 278305987 335374199 50426 SRX1735456 SRS1416509 SRA421168 GEO Oncological Sciences, University of Utah 1 0.91587   0.10088   0.68107   0.48664   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40950 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.   pubmed:27783941   9267X8 tumor GSM2136821   source name:brain tumor|tissue:brain tumor 9267X8 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       284508112 243447832 236471909 285153684 38263 SRX1735455 SRS1416508 SRA421168 GEO Oncological Sciences, University of Utah 1 0.92111   0.10635   0.68061   0.48665   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40951 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.   pubmed:27783941   9267X7 tumor GSM2136820   source name:brain tumor|tissue:brain tumor 9267X7 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       283795799 244445968 237807604 284286043 37936 SRX1735454 SRS1416507 SRA421168 GEO Oncological Sciences, University of Utah 1 0.91684   0.09541   0.70808   0.4782   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40952 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.   pubmed:27783941   9267X6 tumor GSM2136819   source name:brain tumor|tissue:brain tumor 9267X6 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       246296969 211315305 203857359 247684298 33369 SRX1735453 SRS1416506 SRA421168 GEO Oncological Sciences, University of Utah 1 0.92029   0.11221   0.68578   0.47422   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
40953 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.   pubmed:27783941   9267X5 tumor GSM2136818   source name:brain tumor|tissue:brain tumor 9267X5 tumor USeq’s 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’s 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’s 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   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   SRP074122     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       275570887 242993408 235025540 276437064 37651 SRX1735452 SRS1416505 SRA421168 GEO Oncological Sciences, University of Utah 1 0.91852   0.0986   0.70451   0.47961   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-28 Undetermined Undetermined Multi-tissue Multi-system
41035 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.       Fluorescence activated cell sorted macrophages4 iRed4   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed4 iRed4 iRed4 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed4.fastq.gz fastq 2577391029.0 50537079.0 iRed4.fastq.gz 0:51 A:740368299;C:555561208;G:558570747;T:722870515;N:20260 51       740368299 555561208 558570747 722870515 20260 SRX1797273 SRS1465195 SRA429040 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.87886   0.09748   0.75676   0.49364   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Adult Adult Multi-tissue Multi-system
41036 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.       Fluorescence activated cell sorted macrophages3 iRed3   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed3 iRed3 iRed3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed3.fastq.gz fastq 2300094339.0 45099889.0 iRed3.fastq.gz 0:51 A:664396273;C:491535578;G:495836023;T:648307877;N:18588 51       664396273 491535578 495836023 648307877 18588 SRX1797272 SRS1465194 SRA429039 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88281   0.15449   0.75507   0.47198   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Multi-tissue Multi-system
41037 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.       Fluorescence activated cell sorted macrophages2 iRed2   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed2 iRed2 iRed2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed2.fastq.gz fastq 1652550807.0 32402957.0 iRed2.fastq.gz 0:51 A:528348867;C:306088006;G:305625547;T:512475625;N:12762 51       528348867 306088006 305625547 512475625 12762 SRX1797271 SRS1465193 SRA429038 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.83699   0.16858   0.76688   0.49036   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Adult Adult Multi-tissue Multi-system
41363 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3 GSM2339156   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339156 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ243.fq.gz fastq 1057994900.0 21159898.0 GSM2339156 r1 0:50 A:280437817;C:246195249;G:248543608;T:282775343;N:42883 50       280437817 246195249 248543608 282775343 42883 SRX2224020 SRS1731682 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.92441   0.07101   0.73259   0.53564   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41364 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep3 GSM2339155   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339155 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ213.fq.gz fastq 1192895250.0 23857905.0 GSM2339155 r1 0:50 A:311520729;C:281518333;G:288563950;T:311243358;N:48880 50       311520729 281518333 288563950 311243358 48880 SRX2224018 SRS1731680 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.92622   0.06398   0.7315   0.51969   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41365 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae low fat cohort rep3 GSM2339154   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339154 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ203.fq.gz fastq 1333885750.0 26677715.0 GSM2339154 r1 0:50 A:350227472;C:314164789;G:317046609;T:352393122;N:53758 50       350227472 314164789 317046609 352393122 53758 SRX2224017 SRS1731679 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.92695   0.07507   0.72675   0.54558   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41366 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3 GSM2339153   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339153 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ143.fq.gz fastq 3620501750.0 72410035.0 GSM2339153 r1 0:50 A:928100369;C:870292711;G:888545580;T:933466612;N:96478 50       928100369 870292711 888545580 933466612 96478 SRX2224016 SRS1731677 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93833   0.05511   0.75032   0.55771   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41367 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3 GSM2339152   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339152 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ113.fq.gz fastq 2177871950.0 43557439.0 GSM2339152 r1 0:50 A:563893287;C:522092755;G:523081504;T:568747495;N:56909 50       563893287 522092755 523081504 568747495 56909 SRX2224015 SRS1731678 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93698   0.06235   0.75335   0.53049   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41368 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae high fat cohort rep3 GSM2339151   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339151 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ103.fq.gz fastq 1451132900.0 29022658.0 GSM2339151 r1 0:50 A:377007117;C:346007409;G:346873642;T:381206074;N:38658 50       377007117 346007409 346873642 381206074 38658 SRX2224014 SRS1731676 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93743   0.06292   0.74241   0.53805   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41369 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2 GSM2339150   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339150 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ242.fq.gz fastq 1989936500.0 39798730.0 GSM2339150 r1 0:50 A:523392551;C:467800437;G:470494505;T:528201420;N:47587 50       523392551 467800437 470494505 528201420 47587 SRX2224013 SRS1731675 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93233   0.07279   0.72987   0.54632   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41370 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep2 GSM2339149   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339149 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ212.fq.gz fastq 2625058500.0 52501170.0 GSM2339149 r1 0:50 A:685255578;C:619614827;G:635559034;T:684566225;N:62836 50       685255578 619614827 635559034 684566225 62836 SRX2224012 SRS1731674 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93545   0.06765   0.74399   0.53905   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41371 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae low fat cohort rep2 GSM2339148   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339148 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ202.fq.gz fastq 1339075850.0 26781517.0 GSM2339148 r1 0:50 A:350406690;C:316421667;G:317254683;T:354961605;N:31205 50       350406690 316421667 317254683 354961605 31205 SRX2224011 SRS1731672 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93323   0.07254   0.7307   0.55068   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41372 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2 GSM2339147   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339147 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ142.fq.gz fastq 1286162750.0 25723255.0 GSM2339147 r1 0:50 A:346299275;C:294122420;G:300696019;T:345003487;N:41549 50       346299275 294122420 300696019 345003487 41549 SRX2224010 SRS1731671 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.9281   0.07755   0.7305   0.53462   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41373 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep2 GSM2339146   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ112.fq.gz fastq 2002111100.0 40042222.0 GSM2339146 r1 0:50 A:528562099;C:471825161;G:473013263;T:528647491;N:63086 50       528562099 471825161 473013263 528647491 63086 SRX2224009 SRS1731673 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93335   0.07285   0.7419   0.54916   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41374 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae high fat cohort rep2 GSM2339145   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ102.fq.gz fastq 1273490300.0 25469806.0 GSM2339145 r1 0:50 A:331637156;C:303754192;G:304976628;T:333081790;N:40534 50       331637156 303754192 304976628 333081790 40534 SRX2224008 SRS1731670 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93565   0.07655   0.74249   0.54451   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41375 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1 GSM2339144   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ241.fq.gz fastq 2211365050.0 44227301.0 GSM2339144 r1 0:50 A:569415166;C:531526907;G:533692966;T:576677396;N:52615 50       569415166 531526907 533692966 576677396 52615 SRX2224007 SRS1731669 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93633   0.06376   0.73701   0.55588   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41376 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1 GSM2339143   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ211.fq.gz fastq 2627126000.0 52542520.0 GSM2339143 r1 0:50 A:679161674;C:624785100;G:633592207;T:689524385;N:62634 50       679161674 624785100 633592207 689524385 62634 SRX2224006 SRS1731668 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93885   0.06121   0.74629   0.53653   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41377 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae low fat cohort rep1 GSM2339142   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ201.fq.gz fastq 2356799900.0 47135998.0 GSM2339142 r1 0:50 A:604464780;C:566235047;G:573048901;T:612995653;N:55519 50       604464780 566235047 573048901 612995653 55519 SRX2224005 SRS1731667 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93799   0.06151   0.7419   0.54342   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41378 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1 GSM2339141   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ141.fq.gz fastq 2314803100.0 46296062.0 GSM2339141 r1 0:50 A:608880073;C:542117358;G:554834849;T:608902370;N:68450 50       608880073 542117358 554834849 608902370 68450 SRX2224004 SRS1731666 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.9381   0.06487   0.74974   0.53946   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41379 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   1h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep1 GSM2339140   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ111.fq.gz fastq 1178777050.0 23575541.0 GSM2339140 r1 0:50 A:309227949;C:279025719;G:278433554;T:312055796;N:34032 50       309227949 279025719 278433554 312055796 34032 SRX2224003 SRS1731665 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.9381   0.06761   0.74882   0.54735   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
41380 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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.   pubmed:27655916   Unfed 6.5 dpf zebrafish larvae high fat cohort rep1 GSM2339139   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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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   1 At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC.  RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run. GEO Accession:GSM2339139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP090938     EZ101.fq.gz fastq 1628978050.0 32579561.0 GSM2339139 r1 0:50 A:426504328;C:384692513;G:386557023;T:431176784;N:47402 50       426504328 384692513 386557023 431176784 47402 SRX2224002 SRS1731664 SRA482638 GEO Yixian Zheng, Embryology, Carnegie Institution for Science 1 0.93781   0.06883   0.73959   0.52987   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-10-06 Larval Larval Multi-tissue Multi-system
48792 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   Tumor10b GSM3188303   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   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   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   SRP150378     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     207311416 184430035 177791849 208055451 50936 SRX4201621 SRS3411855 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90266   0.11487   0.70485   0.48043   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48793 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   Tumor10a GSM3188302   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   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   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   SRP150378     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     177845565 158702532 152983178 178607700 39157 SRX4201620 SRS3411854 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.8996   0.11677   0.7079   0.47973   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48794 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   Tumor9b GSM3188301   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   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   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   SRP150378     P2_10_ATGTCA_L002_R1_001.fastq.gz fastq 702134340.0 13767340.0 GSM3188301 r1                       SRX4201619 SRS3411853 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90571   0.14513   0.69203   0.47889   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48795 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   Tumor9a GSM3188300   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188300 GSM3188300: Tumor9a; Danio rerio; RNA Seq GSM3188300   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:GSM3188300 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_10_ATGTCA_L001_R1_001.fastq.gz fastq 627573105.0 12305355.0 GSM3188300 r1 0:51 1:0 A:169039407;C:146956335;G:141830873;T:169708780;N:37710 51 0     169039407 146956335 141830873 169708780 37710 SRX4201618 SRS3411852 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.89199   0.13437   0.6981   0.48131   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48796 48796 SRR7299183 SRX4201617 SRS3411851 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   Tumor8b GSM3188299   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188299 GSM3188299: Tumor8b; Danio rerio; RNA Seq GSM3188299   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:GSM3188299 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_09_TGACCA_L002_R1_001.fastq.gz fastq 713031255.0 13981005.0 GSM3188299 r1 0:51 1:0 A:189603634;C:168844651;G:163643823;T:190891262;N:47885 51 0     189603634 168844651 163643823 190891262 47885 SRX4201617 SRS3411851 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90453   0.11706   0.70879   0.47984   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48797 48797 SRR7299182 SRX4201616 SRS3411850 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   Tumor8a GSM3188298   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188298 GSM3188298: Tumor8a; Danio rerio; RNA Seq GSM3188298   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:GSM3188298 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_09_TGACCA_L001_R1_001.fastq.gz fastq 817043613.0 16020463.0 GSM3188298 r1 0:51 1:0 A:217505914;C:193501237;G:187387312;T:218600885;N:48265 51 0     217505914 193501237 187387312 218600885 48265 SRX4201616 SRS3411850 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.89902   0.11683   0.7105   0.47925   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48798 48798 SRR7299181 SRX4201615 SRS3411849 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   Tumor7b GSM3188297   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188297 GSM3188297: Tumor7b; Danio rerio; RNA Seq GSM3188297   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:GSM3188297 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_08_AGTTCC_L002_R1_001.fastq.gz fastq 893345172.0 17516572.0 GSM3188297 r1 0:51 1:0 A:238870325;C:211061647;G:203483952;T:239869870;N:59378 51 0     238870325 211061647 203483952 239869870 59378 SRX4201615 SRS3411849 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90311   0.12385   0.70268   0.4788   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48799 48799 SRR7299180 SRX4201614 SRS3411848 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   Tumor7a GSM3188296   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188296 GSM3188296: Tumor7a; Danio rerio; RNA Seq GSM3188296   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:GSM3188296 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_08_AGTTCC_L001_R1_001.fastq.gz fastq 842756589.0 16524639.0 GSM3188296 r1 0:51 1:0 A:224960485;C:199179838;G:192707044;T:225859142;N:50080 51 0     224960485 199179838 192707044 225859142 50080 SRX4201614 SRS3411848 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.89902   0.12199   0.7022   0.47622   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48800 48800 SRR7299179 SRX4201613 SRS3411847 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   Tumor6b GSM3188295   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188295 GSM3188295: Tumor6b; Danio rerio; RNA Seq GSM3188295   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:GSM3188295 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_07_AGTCAA_L002_R1_001.fastq.gz fastq 839797977.0 16466627.0 GSM3188295 r1 0:51 1:0 A:224019482;C:198671109;G:191964509;T:225086340;N:56537 51 0     224019482 198671109 191964509 225086340 56537 SRX4201613 SRS3411847 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.9038   0.12034   0.71043   0.47766   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48801 48801 SRR7299178 SRX4201612 SRS3411846 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   Tumor6a GSM3188294   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188294 GSM3188294: Tumor6a; Danio rerio; RNA Seq GSM3188294   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:GSM3188294 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_07_AGTCAA_L001_R1_001.fastq.gz fastq 865233870.0 16965370.0 GSM3188294 r1 0:51 1:0 A:230840445;C:204727437;G:197581207;T:232032999;N:51782 51 0     230840445 204727437 197581207 232032999 51782 SRX4201612 SRS3411846 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.89955   0.12066   0.71102   0.4772   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48802 48802 SRR7299177 SRX4201611 SRS3411845 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   Tumor5b GSM3188293   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188293 GSM3188293: Tumor5b; Danio rerio; RNA Seq GSM3188293   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:GSM3188293 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_06_CTTGTA_L002_R1_001.fastq.gz fastq 812489874.0 15931174.0 GSM3188293 r1 0:51 1:0 A:216800449;C:192198794;G:185392447;T:218043753;N:54431 51 0     216800449 192198794 185392447 218043753 54431 SRX4201611 SRS3411845 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90297   0.11797   0.6982   0.47608   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48803 48803 SRR7299176 SRX4201610 SRS3411844 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   Tumor5a GSM3188292   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor5a Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188292 GSM3188292: Tumor5a; Danio rerio; RNA Seq GSM3188292   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:GSM3188292 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_06_CTTGTA_L001_R1_001.fastq.gz fastq 821967969.0 16117019.0 GSM3188292 r1 0:51 1:0 A:219521877;C:194412930;G:187504810;T:220478759;N:49593 51 0     219521877 194412930 187504810 220478759 49593 SRX4201610 SRS3411844 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90248   0.11705   0.69944   0.47763   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48804 48804 SRR7299175 SRX4201609 SRS3411842 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   Tumor4b GSM3188291   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188291 GSM3188291: Tumor4b; Danio rerio; RNA Seq GSM3188291   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:GSM3188291 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_05_CAGATC_L002_R1_001.fastq.gz fastq 740249139.0 14514689.0 GSM3188291 r1 0:51 1:0 A:197140740;C:175546839;G:169412134;T:198100053;N:49373 51 0     197140740 175546839 169412134 198100053 49373 SRX4201609 SRS3411842 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90551   0.11754   0.69264   0.48336   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48805 48805 SRR7299174 SRX4201608 SRS3411843 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   Tumor4a GSM3188290   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor4a Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188290 GSM3188290: Tumor4a; Danio rerio; RNA Seq GSM3188290   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:GSM3188290 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_05_CAGATC_L001_R1_001.fastq.gz fastq 769944093.0 15096943.0 GSM3188290 r1 0:51 1:0 A:204951580;C:182730001;G:176358089;T:205858493;N:45930 51 0     204951580 182730001 176358089 205858493 45930 SRX4201608 SRS3411843 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90377   0.11833   0.69436   0.48968   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48806 48806 SRR7299173 SRX4201607 SRS3411841 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   Tumor3b GSM3188289   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188289 GSM3188289: Tumor3b; Danio rerio; RNA Seq GSM3188289   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:GSM3188289 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_04_GCCAAT_L002_R1_001.fastq.gz fastq 825636858.0 16188958.0 GSM3188289 r1 0:51 1:0 A:219846214;C:195352792;G:189217861;T:221165023;N:54968 51 0     219846214 195352792 189217861 221165023 54968 SRX4201607 SRS3411841 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90614   0.11611   0.7021   0.4783   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48807 48807 SRR7299172 SRX4201606 SRS3411840 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   Tumor3a GSM3188288   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor3a Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188288 GSM3188288: Tumor3a; Danio rerio; RNA Seq GSM3188288   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:GSM3188288 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_04_GCCAAT_L001_R1_001.fastq.gz fastq 814805427.0 15976577.0 GSM3188288 r1 0:51 1:0 A:216908232;C:193172528;G:186799085;T:217877143;N:48439 51 0     216908232 193172528 186799085 217877143 48439 SRX4201606 SRS3411840 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90237   0.11168   0.70256   0.4787   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48808 48808 SRR7299171 SRX4201605 SRS3411838 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   Tumor2b GSM3188287   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor2b Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188287 GSM3188287: Tumor2b; Danio rerio; RNA Seq GSM3188287   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:GSM3188287 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P2_03_ACAGTG_L002_R1_001.fastq.gz fastq 735018069.0 14412119.0 GSM3188287 r1 0:51 1:0 A:195267768;C:174855541;G:168745699;T:196098882;N:50179 51 0     195267768 174855541 168745699 196098882 50179 SRX4201605 SRS3411838 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90685   0.11473   0.71159   0.48328   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48809 48809 SRR7299170 SRX4201604 SRS3411839 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   Tumor2a GSM3188286   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor2a Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor GSM3188286 GSM3188286: Tumor2a; Danio rerio; RNA Seq GSM3188286   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:GSM3188286 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP150378     P1_03_ACAGTG_L001_R1_001.fastq.gz fastq 754160766.0 14787466.0 GSM3188286 r1 0:51 1:0 A:200421484;C:179247287;G:173179205;T:201266219;N:46571 51 0     200421484 179247287 173179205 201266219 46571 SRX4201604 SRS3411839 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90325   0.11248   0.71356   0.4788   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48810 48810 SRR7299169 SRX4201603 SRS3411836 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   Tumor1b GSM3188285   source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor Tumor1b Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   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   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   SRP150378     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     208146136 186789193 180795319 208985840 52285 SRX4201603 SRS3411836 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90541   0.10585   0.71056   0.47843   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
48811 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   Tumor1a GSM3188284   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 “ N 1 t 8 B 4 m 5 A sam split output”. 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   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.   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   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   SRP150378     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     190524485 171176089 164179700 192161274 43756 SRX4201602 SRS3411837 SRA720941 GEO Maura McGrail, GDCB, Iowa State University 1 0.90155   0.10675   0.71019   0.47991   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-06-12 Adult Adult Multi-tissue Multi-system
53027 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+.       Sample6 zic ras tert TR rep3 GSM3937766   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’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. 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   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   SRP214202     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     530371091 316769511 405002707 527096600 100220 SRX6430480 SRS5085640 SRA919726 GEO Computational Biology, ICGEB 1 0.81386   0.19286   0.79066   0.58782   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
53028 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+.       Sample5 zic ras tert TR rep2 GSM3937765   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’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. 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   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   SRP214202     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     540242623 321875714 418515128 537443873 102543 SRX6430479 SRS5085639 SRA919726 GEO Computational Biology, ICGEB 1 0.81011   0.1708   0.79194   0.58047   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
53029 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+.       Sample4 zic ras tert TR rep1 GSM3937764   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’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. 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   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   SRP214202     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     587524426 339600798 441683287 549584233 106195 SRX6430478 SRS5085638 SRA919726 GEO Computational Biology, ICGEB 1 0.77512   0.18858   0.80673   0.59479   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
53030 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+.       Sample3 zic ras rep3 GSM3937763   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’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. 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   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   SRP214202     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     546840565 325717348 423849705 507266868 100977 SRX6430477 SRS5085637 SRA919726 GEO Computational Biology, ICGEB 1 0.80869   0.14118   0.81097   0.59204   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
53031 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+.       Sample2 zic ras rep2 GSM3937762   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’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. 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   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   SRP214202     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     606290106 355481454 458919131 573271976 111946 SRX6430476 SRS5085636 SRA919726 GEO Computational Biology, ICGEB 1 0.80311   0.14529   0.80016   0.61351   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
53032 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+.       Sample1 zic ras rep1 GSM3937761   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’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. 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   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   SRP214202     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     541527209 334145158 434769924 529718084 102550 SRX6430475 SRS5085635 SRA919726 GEO Computational Biology, ICGEB 1 0.83576   0.15359   0.79555   0.59782   101   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk unknown unknown   Unknown 2019-07-11 Adult Adult Multi-tissue Multi-system
59351 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchE library 10 batchE stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       131858438 155399854 158242625 165382769 9212 SRX8413250 SRS6725560 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.07236   0.0163   0.95574   0.71914   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59352 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchE library 9 batchE control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       145919628 180332988 185160654 169595863 10019 SRX8413249 SRS6725559 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.03361   0.00721   0.97585   0.72421   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59353 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchD library 8 batchD stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       223839245 210712788 239626812 207623100 12967 SRX8413248 SRS6725558 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.01456   0.00285   0.98685   0.79954   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59354 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchD library 7 batchD control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       187309754 240910478 236157154 207547961 12335 SRX8413247 SRS6725557 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.00388   0.00062   0.99622   0.86525   66   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59355 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchC library 6 batchC stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       138378307 145942814 162208729 141818898 8846 SRX8413246 SRS6725556 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.02473   0.00511   0.98317   0.76412   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59356 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchC library 5 batchC control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       153195532 210035381 176169980 184660888 10227 SRX8413245 SRS6725555 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.02036   0.00355   0.98265   0.71654   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59357 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchB library 4 batchB stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       176688644 183414624 192032878 182569784 10888 SRX8413244 SRS6725554 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.03816   0.00665   0.97378   0.80915   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59358 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchB library 3 batchB control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       141927022 169937693 166391833 161342157 9473 SRX8413243 SRS6725553 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.00358   0.00027   0.99857   0.92025   66   T   under 1.2% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59359 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchF library 12 batchF stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       197687950 209840385 245135169 204114009 12377 SRX8413242 SRS6725552 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.13729   0.02049   0.93752   0.71536   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59360 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchF library 11 batchF control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       215219357 226988408 230348786 218445888 13137 SRX8413241 SRS6725551 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.10021   0.02466   0.95789   0.65844   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59361 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.       Small RNA seq of zebrafish spermatozoa from stressed adult male batchA library 2 batchA stress   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       198694732 195900186 206731529 189432489 11748 SRX8413240 SRS6725550 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.06132   0.01001   0.96731   0.807   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59362 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.       Small RNA seq of zebrafish spermatozoa from control adult male batchA library 1 batchA control   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                 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…     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP265077     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       180861950 199407609 204723388 211390521 11472 SRX8413239 SRS6725549 SRA1080712 University of Tartu|Department of Pathophysiology University of Tartu 1 0.01922   0.00235   0.99024   0.87449   66   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Estonia 2020-05-28 Adult Adult Multi-tissue Multi-system
59501 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.   pubmed:32912962   Adult tail 2 GSM4591062   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   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   tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591062 GSM4591062: Adult tail 2; Danio rerio; OTHER GSM4591062   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   SRP265951   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       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   0.20653   0.88722   0.58074   37   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Adult Adult Multi-tissue Multi-system
59502 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.   pubmed:32912962   Adult tail 1 GSM4591061   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   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   tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591061 GSM4591061: Adult tail 1; Danio rerio; OTHER GSM4591061   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   SRP265951   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       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   0.12127   0.91806   0.67424   44   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Adult Adult Multi-tissue Multi-system
67129 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3G S14 GSM5711820   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711820 GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq GSM5711820   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     163825101 138603508 155901420 152120085 4136 SRX13284817 SRS11197574 SRA1337575 GEO US EPA 1 0.95929   0.11356   0.72354   0.52498   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67130 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3G S14 GSM5711820   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711820 GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq GSM5711820   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     159210709 134719825 151432112 147848359 2470 SRX13284817 SRS11197574 SRA1337575 GEO US EPA 1 0.95964   0.11339   0.72445   0.52239   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67131 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3G S14 GSM5711820   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711820 GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq GSM5711820   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     160858296 136155437 153190178 149240819 3795 SRX13284817 SRS11197574 SRA1337575 GEO US EPA 1 0.95904   0.11412   0.72533   0.5151   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67132 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3G S14 GSM5711820   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711820 GSM5711820: GRC350 D5 3G S14; Danio rerio; RNA Seq GSM5711820   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     158219859 133806362 150430635 146895878 3341 SRX13284817 SRS11197574 SRA1337575 GEO US EPA 1 0.95902   0.11344   0.72468   0.52555   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67133 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3F S10 GSM5711819   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711819 GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq GSM5711819   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     120833503 101700505 110413638 120555105 77224 SRX13284816 SRS11197573 SRA1337575 GEO US EPA 1 0.94667   0.09349   0.70676   0.47641   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67134 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3F S10 GSM5711819   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711819 GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq GSM5711819   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     117659308 99057961 107463452 117396067 68962 SRX13284816 SRS11197573 SRA1337575 GEO US EPA 1 0.94671   0.09333   0.70666   0.47464   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67135 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3F S10 GSM5711819   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711819 GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq GSM5711819   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     119957953 101154236 109745090 119627796 35050 SRX13284816 SRS11197573 SRA1337575 GEO US EPA 1 0.94629   0.0931   0.70603   0.47769   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67136 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3F S10 GSM5711819   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711819 GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq GSM5711819   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     117881601 99242228 107863727 117545157 35087 SRX13284816 SRS11197573 SRA1337575 GEO US EPA 1 0.94519   0.09359   0.7069   0.46281   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67137 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3D S11 GSM5711818   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711818 GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq GSM5711818   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     132860149 113519137 131829845 118135255 3364 SRX13284815 SRS11197571 SRA1337575 GEO US EPA 1 0.96017   0.11843   0.74061   0.5142   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67138 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3D S11 GSM5711818   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711818 GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq GSM5711818   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     128841184 110129820 127873134 114636382 1855 SRX13284815 SRS11197571 SRA1337575 GEO US EPA 1 0.96092   0.12068   0.74036   0.48436   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67139 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3D S11 GSM5711818   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711818 GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq GSM5711818   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     129166672 110526807 128392727 114738937 2882 SRX13284815 SRS11197571 SRA1337575 GEO US EPA 1 0.96019   0.1208   0.74132   0.51095   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67140 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3D S11 GSM5711818   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711818 GSM5711818: GRC350 D5 3D S11; Danio rerio; RNA Seq GSM5711818   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     127801747 109250038 126854910 113607491 2639 SRX13284815 SRS11197571 SRA1337575 GEO US EPA 1 0.96058   0.12042   0.7403   0.51486   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67141 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3C S8 GSM5711817   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711817 GSM5711817: GRC350 D5 3C S8; Danio rerio; RNA Seq GSM5711817   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     122121827 104607471 119890528 114785157 76542 SRX13284814 SRS11197572 SRA1337575 GEO US EPA 1 0.961   0.1222   0.73434   0.52729   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system
67142 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 µM 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 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL 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 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and sc…       GRC350 D5 3C S8 GSM5711817   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 ≤ 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 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL 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 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 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°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM 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™ 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 μl. 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. 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 fish/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°C and bred every 2–3 weeks. For embryo collection 60–100 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 30–40 min later. treatment:potassium perfluorohexane 1 sulfonate|concentration µm:7.87|age:5 dpf stage:larvae|strain:mixed wildtype GSM5711817 GSM5711817: GRC350 D5 3C S8; Danio rerio; RNA Seq GSM5711817   1 Each pooled sample underwent RNA extraction using Direct zol™ 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 μl. 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   SRP348912     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     119747169 102604108 117644135 112565022 69366 SRX13284814 SRS11197572 SRA1337575 GEO US EPA 1 0.96165   0.12333   0.73273   0.52955   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   United States 2021-12-02 Larval Larval Multi-tissue Multi-system

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