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 36482,SRR530894,SRX172598,SRS352620,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 3,GSM979608,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979608,GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq,GSM979608 1,GSM979608: 60hpf TCDD 3,1,,GEO Accession:GSM979608,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,,,1007239870.0,28778282.0,GSM979608 r1,0:35,0:284531587;1:248579138;2:213782485;3:258771962;.:1574698,35,,,,,,,,,SRX172598,SRS352620,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04824,,0.03,,0.981,,0.49967,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36483,SRR530893,SRX172597,SRS352619,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 2,GSM979607,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979607,GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq,GSM979607 1,GSM979607: 60hpf TCDD 2,1,,GEO Accession:GSM979607,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0011.csfasta,SOLiD_native,407347325.0,11638495.0,GSM979607 r1,0:35,0:99062820;1:113921998;2:81336108;3:112422342;.:604057,35,,,,,,,,,SRX172597,SRS352619,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04258,,0.02455,,0.98287,,0.5048,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36484,SRR530892,SRX172596,SRS352618,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 1,GSM979606,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979606,GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq,GSM979606 1,GSM979606: 60hpf TCDD 1,1,,GEO Accession:GSM979606,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0010.csfasta,SOLiD_native,680837045.0,19452487.0,GSM979606 r1,0:35,0:165079839;1:167219862;2:147812329;3:199659766;.:1065249,35,,,,,,,,,SRX172596,SRS352618,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.02295,,0.01479,,0.98884,,0.55191,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36485,SRR530891,SRX172595,SRS352617,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 3,GSM979605,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979605,GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq,GSM979605 1,GSM979605: 60hpf DMSO 3,1,,GEO Accession:GSM979605,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0009.csfasta,SOLiD_native,495019840.0,14143424.0,GSM979605 r1,0:35,0:134854583;1:126192934;2:102458221;3:130747961;.:766141,35,,,,,,,,,SRX172595,SRS352617,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.06707,,0.04409,,0.97285,,0.5058,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36486,SRR530890,SRX172594,SRS352616,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 2,GSM979604,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979604,GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq,GSM979604 1,GSM979604: 60hpf DMSO 2,1,,GEO Accession:GSM979604,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0008.qual,SOLiD_native,440403425.0,12582955.0,GSM979604 r1,0:35,0:110302240;1:106481197;2:104551283;3:118415637;.:653068,35,,,,,,,,,SRX172594,SRS352616,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05778,,0.03522,,0.97423,,0.50884,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36487,SRR530889,SRX172593,SRS352615,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 1,GSM979603,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979603,GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq,GSM979603 1,GSM979603: 60hpf DMSO 1,1,,GEO Accession:GSM979603,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0007.csfasta MH_0007.qual,SOLiD_native SOLiD_native,583800490.0,16680014.0,GSM979603 r1,0:35,0:166122108;1:149534173;2:111986455;3:155255262;.:902492,35,,,,,,,,,SRX172593,SRS352615,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05644,,0.03829,,0.9781,,0.4997,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36687,SRR801685,SRX258166,SRS406297,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Pec fin stage,GSM1112161: Pec fin 60hpf,GSM1112161,,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,Pec fin 60hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Pec fin stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,GSM1112161,GSM1112161: Pec fin 60hpf; Danio rerio; RNA Seq,GSM1112161 1,,1,,GEO Accession:GSM1112161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_60hpf_rep1_F3_QV.qual.bz2 D_rerio_60hpf_rep1_F3.csfasta.bz2,SOLiD_native SOLiD_native,14061264450.0,281225289.0,GSM1112161 r1,0:50,0:3272552510;1:3838757055;2:3984098731;3:2865843173;.:100012981,50,,,,,,,,,SRX258166,SRS406297,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.64298,,0.04687,,0.8452,,0.50527,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36688,SRR801686,SRX258166,SRS406297,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Pec fin stage,GSM1112161: Pec fin 60hpf,GSM1112161,,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,Pec fin 60hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Pec fin stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,GSM1112161,GSM1112161: Pec fin 60hpf; Danio rerio; RNA Seq,GSM1112161 1,,1,,GEO Accession:GSM1112161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_60hpf_rep2_F3.csfasta.bz2 D_rerio_60hpf_rep2_F3_QV.qual.bz2,SOLiD_native SOLiD_native,4988485300.0,99769706.0,GSM1112161 r2,0:50,0:1195740374;1:1346591727;2:1390300069;3:1024571482;.:31281648,50,,,,,,,,,SRX258166,SRS406297,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.65039,,0.04382,,0.84463,,0.50042,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36689,SRR801684,SRX258165,SRS406296,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Long pec stage,GSM1112160: Long pec 48hpf,GSM1112160,,strain:AB|developmental stage:Long pec 48hpf|tissue:embryo,Long pec 48hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Long pec stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Long pec 48hpf|tissue:embryo,GSM1112160,GSM1112160: Long pec 48hpf; Danio rerio; RNA Seq,GSM1112160 1,,1,,GEO Accession:GSM1112160,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_48hpf_F3.csfasta.bz2 D_rerio_48hpf_F3_QV.qual.bz2,SOLiD_native SOLiD_native,18932266250.0,378645325.0,GSM1112160 r1,0:50,0:4346139923;1:5132091383;2:5261012454;3:4060753494;.:132268996,50,,,,,,,,,SRX258165,SRS406296,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.59799,,0.03168,,0.87787,,0.49407,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures