run_metadata: 56090

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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
56090	SRR10868195	SRX7538218	SRS5976882	SRP241164	PRJNA600413	Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome	GSE143416	Transcriptome Analysis	Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.		pubmed:33163595		CTFB rep1	GSM4259015		source name:Control Female Brain 1\|strain:short fin 'AB' strain\|condition:Control\|Sex:female\|tissue:Brain	CTFB rep1	Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues	Control Female Brain 1	For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.	Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.	Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.	strain:short fin 'AB' strain\|condition:Control\|Sex:Female\|tissue:Brain	GSM4259015	GSM4259015: CTFB rep1; Danio rerio; RNA Seq	GSM4259015		1	Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.	GEO Accession:GSM4259015	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP241164			CTFB1_R1.fastq.gz CTFB1_R2.fastq.gz	fastq fastq	7268191400.0	36340957.0	GSM4259015 r1	0:100 1:100	A:2025221999;C:1631297953;G:1641821598;T:1966011517;N:3838333	100	100			2025221999	1631297953	1641821598	1966011517	3838333	SRX7538218	SRS5976882	SRA1023469	GEO	CSIR Centre for Cellular and Molecular biology	2	0.93943	0.93735	0.12747	0.12896	0.68925	0.69475	0.51438	0.50946	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		India	2020-01-10	Juvenile	Juvenile	Brain	Nervous System