run_metadata: 35889

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
35889	SRR33167516	SRX28428336	SRS24751209	SRP579141	PRJNA1251588	Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish	GSE294778	Transcriptome Analysis	Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.				MB125 3F L7.D706	GSM8919419		source name:pooled heads collected anterior to swim bladder of larval zebrafish\|tissue:pooled heads collected anterior to swim bladder of larval zebrafish\|strain:mixed wild type zebrafish line US EPA\|lifestage:larvae\|age:10 dpf colonized with microbes control\|experiment:1\|geo loc name:missing\|collection date:missing	MB125 3F L7.D706	For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples	pooled heads collected anterior to swim bladder of larval zebrafish		Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.		tissue:pooled heads collected anterior to swim bladder of larval zebrafish\|strain:mixed wild type zebrafish line US EPA\|lifestage:larvae\|age:10 dpf colonized with microbes control\|experiment:1	GSM8919419	GSM8919419: MB125 3F L7.D706; Danio rerio; RNA Seq	GSM8919419 r1	GSM8919419	1	Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP579141			MB125_3F_L7.D706_1.fastq.gz MB125_3F_L7.D706_2.fastq.gz	fastq fastq	2752811598.0	26988349.0	GSM8919419 r1	0:51 1:51	A:667499048;C:689713749;G:683954270;T:711568265;N:76266	51	51			667499048	689713749	683954270	711568265	76266	SRX28428336	SRS24751209	SRA2113523	US EPA	US EPA												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk		United States	2025-04-16	Larval	Larval	Multi-tissue	Multi-system