run_metadata: 59329

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
59329	SRR11856748	SRX8406847	SRS6719210	SRP264975	PRJNA635397	Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf	GSE151291	Transcriptome Analysis	Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.				5 dpf Untreated liver clutch 2	GSM4572114		tissue:Liver\|genotype:Tgfabp10a:ER tdTomato\|pool:20	5 dpf Untreated liver clutch 2	Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes	Liver	At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.	Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.	At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.	genotype:Tgfabp10a:ER tdTomato\|pool:20\|rna qbit concentrationng/ul:17.4	GSM4572114	GSM4572114: LIV UT 2; Danio rerio; RNA Seq	GSM4572114		1	20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar	GEO Accession:GSM4572114	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP264975			LIV_UT_2_S12_read1.fastq.gz LIV_UT_2_S12_read2.fastq.gz	fastq fastq	5896961329.0	20821534.0	GSM4572114 r1	0:141.54 1:141.67	A:1594568853;C:1356093648;G:1372236539;T:1573104763;N:957526	141	141			1594568853	1356093648	1372236539	1573104763	957526	SRX8406847	SRS6719210	SRA1080364	GEO	Biology, New York University Abu Dhabi	2	0.94954	0.95239	0.04824	0.0487	0.82363	0.83011	0.55109	0.56041	140	140	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	bulk	bulk	bulk		United Arab Emirates	2020-05-27	Larval	Larval	Liver	Liver and Biliary System