{"database": "metadata", "table": "run_metadata", "rows": [[49783, "SRR8040480", "SRX4870992", "SRS3925972", "SRP165278", "PRJNA495918", "Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish", "GSE121164", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 \u00b0C compared to fish kept at constant 28 \u00b0C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct9 miRNA seq", "GSM3427259", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct9 miRNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 \u00b0C for 2 min  1 cycle; 95 \u00b0C for 20 s  60 \u00b0C for 30 s  72 \u00b0C for 15 s  22 cycles; 72 \u00b0C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427259", "GSM3427259: t32ct9 miRNA seq; Danio rerio; miRNA Seq", "GSM3427259", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 \u00b0C for 2 min  1 cycle; 95 \u00b0C for 20 s  60 \u00b0C for 30 s  72 \u00b0C for 15 s  22 cycles; 72 \u00b0C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427259", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165278", null, null, null, null, 2182814316.0, 28721241.0, "GSM3427259 r1", "0:76 1:0", "A:538572480;C:545202669;G:589186456;T:509834541;N:18170", 76, 0, null, null, 538572480, 545202669, 589186456, 509834541, 18170, "SRX4870992", "SRS3925972", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00546, null, 0.00069, null, 0.99466, null, 0.54142, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["49783"], "units": {}, "query_ms": 11.117103997094091}