{"database": "metadata", "table": "run_metadata", "rows": [[62625, "SRR13249699", "SRX9681374", "SRS7879223", "SRP297857", "PRJNA685060", "Transcriptome of Zebrafish Intestine under Fe'i and Cavendish Banana Diet", "GSE163139", "Transcriptome Analysis", "Fe'i banana Musa troglodytarum fruit is carotenoid rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish Danio rerio intestine that were subjected to 8 weeks of Fe'i banana and Cavendish Musa acuminata diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity. Overall design: Adult healthy zebrafish were divided into 3 diet groups: commercial feed CO  Cavendish CV  and Fe'i banana FE. Zebrafish in commercial feed diet group was used as control and fed Tetramin Tetra  Germany. Ripe Cavendish and Fe'i fruit pulp were mixed with commercial feed into 50% banana containing granule by lyophilization. Treatment lasted for 8 weeks. At day 56  total RNA of intestine from each diet group were sequenced. Transcriptome assembly were done using Tophat Cufflink pipeline.", null, null, null, "Zebrafish Intestine   CV", "GSM4972508", null, "tissue:intestine|Stage:Day 56 of diet treatment|treatment:Cavendish diet 50% Tetramin  50% Cavendish fruit pulp|organ:intestine", "Zebrafish Intestine   CV", "Raw paired end reads were examined for base score  adapter content  and overrepresented sequences with FastQC v0.11.5 Clean reads were aligned to zebrafish genome reference using Tophat2 v2.1.0 with default parameters Transcriptome assembly and gene expression quantification were calculated with Cufflink v2.2.1 in default parameters. Abundance were calculated in fragments per kilobase of transcript per million reads FPKM. Genes were considered differentially expressed if log2FC>1.5 Genome build: Danio rerio GRCz11 GCA 000002035.4 Supplementary files format and content: tab deliminated files containing gene ID  gene short name  locus  and FPKM", "intestine", "Zebrafish were divided into 3 treatment groups  i.e. control  Cavendish diet  and Fe'i diet. Control zebrafish CO were fed commercial feed Tetramin Tetra  Germany. Zebrafish in Cavendish diet group CV received Cavendish containing granule. Similarly  zebrafish in Fe'i diet group FE were fed Fe'i containing granule. Banana containing granule were prepared from fruit pulp according to Tanaika et al. 2011. The resulting granule contains 50% banana fruit pulp to Tetramin. All feeds were given as much as 4% of body weight per day  divided into three daily feedings.", "Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1\u00b5g of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina", "Healthy adult zebrafish of 6 mpf 9 mpf were maintained under established protocols Avdesh et al.  2012. Lightning conditions were 14:10 hour light:dark.", "Stage:Day 56 of diet treatment|treatment:Cavendish diet 50% Tetramin  50% Cavendish fruit pulp|organ:intestine", "GSM4972508", "GSM4972508: Zebrafish Intestine   CV; Danio rerio; RNA Seq", "GSM4972508", null, "1", "Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1\u00b5g of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina", "GEO Accession:GSM4972508", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP297857", null, null, "RNA-CV_1.fq.gz RNA-CV_2.fq.gz", "fastq fastq", 8700195600.0, 29000652.0, "GSM4972508 r1", "0:150 1:150", "A:2300738433;C:2030008598;G:2063236046;T:2305470240;N:742283", 150, 150, null, null, 2300738433, 2030008598, 2063236046, 2305470240, 742283, "SRX9681374", "SRS7879223", "SRA1173924", "GEO", "School of Life Sciences and Technology, Institut Teknologi Bandung", 2, 0.91916, 0.91872, 0.04907, 0.04902, 0.75595, 0.76051, 0.50144, 0.50578, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Indonesia", "2020-12-14", "Juvenile", "Juvenile", "Gut", "Digestive 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": ["62625"], "units": {}, "query_ms": 8.971534996817354}