run_metadata: 41252

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
41252	SRR3987430	SRX1989727	SRS1593549	SRP080353	PRJNA335856	High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish	GSE85004	Transcriptome Analysis	Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.				CON F1	GSM2255737		source name:F1 zebrafish 7 dpf F0 0 mg/L DKA exposure\|strain/background:AB\|genotype/variation:WT\|f0 treatment:0 mg/L DKA exposure for 90 days\|tissue:F1 whole body\|f1 developmental stage:7 dpf	CON F1	Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the predicted hairpin >=12; and 11 percent of mature in stem >=80. For normalized abundance measurements a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are: 1. There is a subset of sequences of a significant number that do not change significantly across all samples. 2. In sequencing measurements experimental condition variations may lead to copy number reading variations. However in each sample run the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample. Genome build: Zv9 ftp://ftp.ensembl.org/pub/release 66/fasta/danio rerio/dna/ Supplementary files format and content: Table8.2 S12 F1vsS6 F1vsCON F1.xlsx indicates the differential expression between two DKA exposure treatments 6.25 and 12.5 mg/L treatments and control. Supplementary files format and content: Table8.6 S12 F1vsS6 F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA exposure treatments. Supplementary files format and content: Table8.7 S6 F1vsCON F1.xlsx indicates the differential expression between 6.25 mg/L DKA exposure treatment and control. Supplementary files format and content: Table8.8 S12 F1vsCON F1.xlsx indicates the differential expression between 12.5 mg/L DKA exposure treatment and control.	F1 zebrafish 7 dpf F0 0 mg/L DKA exposure	Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%.	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.		strain/background:AB\|genotype/variation:WT\|f0 treatment:0 mg/L DKA exposure for 90 days\|tissue:F1 whole body\|f1 developmental stage:7 dpf	GSM2255737	GSM2255737: CON F1; Danio rerio; ncRNA Seq	GSM2255737		1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.	GEO Accession:GSM2255737	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP080353			CON_F1.fq	fastq	505867350.0	10117347.0	GSM2255737 r1	0:50	A:123471791;C:114424623;G:138931875;T:129020913;N:18148	50				123471791	114424623	138931875	129020913	18148	SRX1989727	SRS1593549	SRA446490	GEO	Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province	1	2e-05		0.0		0.99993		0.66666		50		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown		China	2016-07-29	Larval	Larval	Trunk	Surface Structure