run_metadata: 62625

This data as json

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
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.				Zebrafish Intestine CV	GSM4972508		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. 1µg 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		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. 1µg 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		SRP297857			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			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		Indonesia	2020-12-14	Juvenile	Juvenile	Gut	Digestive System