{"database": "metadata", "table": "run_metadata", "rows": [[49758, "SRR8040442", "SRX4870954", "SRS3925988", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. 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, "t28lps8 RNA seq", "GSM3427224", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps8 RNA 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 mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 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", "GSM3427224", "GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq", "GSM3427224", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427224", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2342903700.0, 31238716.0, "GSM3427224 r1", "0:75 1:0", "A:613986696;C:535703169;G:527411229;T:665771221;N:31385", 75, 0, null, null, 613986696, 535703169, 527411229, 665771221, 31385, "SRX4870954", "SRS3925988", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92238, null, 0.11108, null, 0.75223, null, 0.54609, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "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": ["49758"], "units": {}, "query_ms": 8.801788004348055}