{"database": "metadata", "table": "run_metadata", "rows": [[39715, "SRR2067882", "SRX1063362", "SRS963398", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL  namely the lower end of survival temperature  is an important trait delimiting the geographical distribution of a species  however  the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus  which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure  forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently  we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia  corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 28 gill 2", "GSM1714079", null, "source name:gill|age:6 months|tissue:gill|group:9|replicate:2|condition:28\u00b0C|temperature:28\u00b0C", "zebrafish 28 gill 2", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First  the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then  the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20  and post trimming length of 50 bases or longer are enforced. Finally  the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h  to 8\u00b0C  and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C  tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C  0h of LOE 6h of LOE and 12h of LOE  gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition  post 6h of LOE  tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:9|replicate:2|condition:28\u00b0C|temperature:28\u00b0C", "GSM1714079", "GSM1714079: zebrafish 28 gill 2; Danio rerio; RNA Seq", "GSM1714079", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_28_gill_2_2.fq.gz zebrafish_28_gill_2_1.fq.gz", "fastq fastq", 2621117986.0, 12023477.0, "GSM1714079 r1", "0:109 1:109", "A:690118661;C:623432564;G:622600619;T:684797673;N:168469", 109, 109, null, null, 690118661, 623432564, 622600619, 684797673, 168469, "SRX1063362", "SRS963398", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.90329, 0.90413, 0.08957, 0.09004, 0.67529, 0.67673, 0.49233, 0.49384, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory 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": ["39715"], "units": {}, "query_ms": 10.441863996675238}